September 2007 - Mg-rast - mailman3.cels.anl.gov

mg-rast Fwd: [rast] [Fwd: ] rast server login
by Gordon D. Pusch 20 Sep '07

20 Sep '07

Bill --- FYI, I'm passing this on to <mg-rast(a)mcs.anl.gov> (the Metagenomics RAST list). Begin forwarded message: > From: William Mihalo <wmihalo(a)ci.uchicago.edu> > Date: September 20, 2007 8:48:13 AM CDT > To: rast(a)mcs.anl.gov > Subject: [rast] [Fwd: ] rast server login > > forwarded from info(a)theseed.org > > From: Isabelle Navarro <Elisabeth.Navarro(a)ec-lyon.fr> > Date: September 20, 2007 3:42:31 AM CDT > To: info(a)theseed.org > > > Hello, > > Last week, I tried to create an account in order to used the > Metagenomics RAST Server. Nevertheless, I never received the login > and the password. I would like to uses SEED in order to analyze > metagenomic data and I really appreciate if you coud give a login > and a password > > > Thanks, sincerely yours > > Elisabeth Navarro > > > Elisabeth.Navarro(a)ec-lyon.fr > Equipe « Génomique Microbienne Environnementale » (Environmental > Microbial Genomics Group ) > UMR CNRS 5005, Laboratoire Ampère, Ecole Centrale de Lyon , 36 > avenue Guy de Collongue, 69134 Ecully Cedex, France > > www.GenomEnviron.org

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mg-rast Re: Questions about mg rast
by Daniel Paarmann 19 Sep '07

19 Sep '07

Jack, > the submission of sequences to SEED appears to of changed. It is > coming up with a genome centric submission which seems to have no > place for metagenomic samples. thank you for notifying us about this. It has been corrected and the metagenome RAST server shows the correct upload page again. Unfortunately, due to this configuration error on our side, your jobs 202-205 have been created as regular RAST jobs. I had to delete them and would ask you to upload them again. My apologies for any inconvenience this may cause. 202 All All All 203 Bag1 13thMay cDNA 204 Bag6 19thMay cDNA 205 Bag1 19thMay cDNA > Also, quick question regarding the taxanomic analysis, the > taxanomic analysis data keeps on changing - at least everytime I > look at it I see problems or things that have changed. Is this in > continuous flux? The taxonomic analysis and the databases used for it have not been changed since the server release. We appreciate any feedback about inconsistencies and will investigate it immediately. Could you be more specific for what metagenome (job) you noticed differences? What kind of changes did you observe? Regarding your question how to delete jobs, this action is currently not supported by the RAST web service, but I will suggest it for our next release. For now, if you send my the job numbers and metagenome ids, I'll gladly delete them for you. Best regards, Daniel Paarmann

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Re: mg-rast making a production server
by Robert Olson 17 Sep '07

17 Sep '07

And we are back online. The usual metagenomics.nmpdr.org URL points to /vol/metagenome-48-hour/FIGdisk.prod and FIGdisk.backend.prod, which uses the jobs in Jobs.prod. http://treponema.nmpdr.org/48-hour-dev/FIG/rast.cgi points to .dev versions with jobs in Jobs.dev. --bob On Mon, 17 Sep 2007, Robert Olson wrote: > I am snapshotting the current dev and only mgrast server to call it > the first cut at a production server. I am going to idle the > processing of the pipeline in order to make a clean cutover after the > current jobs finish. this should be done by the morning. > >

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mg-rast making a production server
by Robert Olson 17 Sep '07

17 Sep '07

I am snapshotting the current dev and only mgrast server to call it the first cut at a production server. I am going to idle the processing of the pipeline in order to make a clean cutover after the current jobs finish. this should be done by the morning.

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Re: mg-rast Re: 454 - account already made for Bergen data
by Folker Meyer 17 Sep '07

17 Sep '07

On Sep 17, 2007, at 10:37 AM, Jack Gilbert wrote: > Folker, > > One more thing. The taxanomic heat map....how is it constructed, > what taxanomic affiliation does it use to infer relative abundance, > protein BLAST hits or some kind of phylogenetic marker? > Jack: there is actually two pages: - one with a 16s based phylogenetic reconstruction (using one of 3 databases: GREENGENES, RDP-ii, and the euro 16s DB) - the other is looking at protein blastp hits and their source organisms Cheers, Folker > Cheers > > Jack > > > On 9/17/07, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > Folker or Rob, > > Is there any reason why I might get an incomplete blast search > results page...it looks like when i search against our data it > returns nothing....even for genes that SEED suggests are found in > the data. > > Link fault? > > Let me know > > jack > > > On 9/17/07, Jack Gilbert <gilbertjack(a)gmail.com > wrote: > folker, > > I agree with dawn, but would go further to suggest that a sequence > identity matrix (% identity for each) for the 16S seqs from each > pyroseq run would be a great, it would mean that we would not have > to pull out individual 16S seqs and run this operation here. > > Dawn, > > You submitted 630 and 632 to the SEED it has been run with the new > database, hence the 64% sequences found in the database. > > I have uploaded the new seqs to SEED hopefully these will be done > by tomorrow, if not by today. > > re. clustering, lets talk about this tomorrow. It might give us > something interesting and if there is a less labour intensive way > of doing it then I would jump on it. However, it might not. There > is no real link between what clustering tells us and the > statistical analysis performed by Rob, which I was surprised about. > anyway talk about this tomorrow. > > There was a small prob with the pyro run from Liverpool and so we > have got less than an anticipated but he is re running the samples > and hopefully will get it sorted, so should end up with more than > we requested. DNA will be done soon as well....this is essential > for the comparison between GC-20 and Flx...that is supposed to be > done by end of this week...fingers crossed. > > I will have a word with Neil, but he is going away for a while, so > will have to see how long it will take. > > folker, thank you for your help, I am keen to see what would happen > when silva is introduced....although the short seq reads might > cause F-O and Wolfgang some consternation! > > Cheers > > Jack > > > > > On 9/17/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Doh...forgot who I > was talking to :-) Great if Silva can be grabbed - do you have a > timeline? > > Yes, it would be fabulous to meet up. You are more than welcome to > visit Oxford. We can set you up a seminar or do something more > casual - where will you be? > > We should get initial feedback on the river microbe proposal next > week and a more final decision next month - I think they will come > back to PIs for more information - and knowing updates to the SEED > will be really helpful. > > I don't know if Rob had time to debrief you from the US-EU Task > force but Stefan Schuster presented on MEGAN. I think he and Rob > worked out a way to build a plugin to the SEED that would output > data ready for viewing in MEGAN - just to confirm we'd be really > keen on this. > > Also really keen on having on diversity matrix ( samples in > columns, taxa in rows, in a square matrix) produced from that > taxonomy analysis but perhaps downstream after sliva (as we can > manually make these here) and fasta files of just 16S (maybe this > is already there, just haven't seen it). > > Dawn > > >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> > Dear Dawn, > > I will send an email to Frank Oliver. > > > Cheers, > Folker > PS: I am planning to be in Europe some time in early November for a > workshop. If there is any reason to meet that would be a good time. > > On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > > > Dear Folker, > > > > I don't know if Rob has already mentioned this but we would really > > love to have the Silva database behind SEED for the sake of making > > taxonomic assignments. > > > > http://www.arb-silva.de/ > > > > It is great, the largest 16S database around now, actively > > developed and has all three domains. Rob thought it was a good > > idea too :-) > > > > If you don't already have connections, we can put you in touch with > > the developers if there are any issues to clarify before > > considering it. > > > > I assume (?) it's as simple as downloading and putting another > > option in the pipeline? > > > > Dawn > > > > > > > >>>> Folker Meyer < folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > > Jack: > > > > so ensure compatibility we did run all old metagenomes against a > > stable version of our internal databases. > > > > Now we updated all DBs used for analysis. The first runs were > > previously analyzed with a rather ancient version of our NR (non > > redundant protein database) and also a very old subsystem > collection. > > > > This explains the dramatic change. The current subsystem collection > > has more than 600 subsystems (old one had significantly less) and > > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > > etc... > > > > Hope that helps, > > Folker > > > > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > > > >> Rob and/or mg-rast techs. > >> > >> just looking at the sequencing data from the first 454 runs (Bag1 > >> and Bag6, 630 and 632) and the number of sequences that are found > >> within subsystem catagories has leapt from 24% to 64%.....this > >> seems amazing to me. > >> > >> Does this mean that SEED has suddenly expanded to include a lot > >> more information or is this due to a new analysis > >> technique...interested to know. > >> > >> Jack > >> > >> > >> On 9/14/07, Rob Edwards < raedwards(a)gmail.com> wrote: Jack, Dawn, > >> > >> I'm forwarding this to our internal mailing list for developers > that > >> work on the metagenomics RAST for two reasons - its great to see > some > >> praise once in a while in amongst all the people that get stuck or > >> have problems, and also because they can answer all the > specifics of > >> what is being done and how. > >> > >> Rob > >> > >> > >> > >> Begin forwarded message: > >> > >>> From: "Jack Gilbert" < gilbertjack(a)gmail.com> > >>> Date: September 14, 2007 4:51:31 AM PDT > >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> > >>> Cc: raedwards(a)gmail.com > >>> Subject: Re: 454 - account already made for Bergen data > >>> > >>> Dawn and Rob, > >>> > >>> I know I saw all the menus but from my end I can only see the > >>> diversity info for protein sequences not for rdp, green genes or > >> ERD. > >>> > >>> I agree the taxanomic comprison heatmap is fantastic. However, > what > >>> is used to construct it? > >>> > >>> Jack > >>> > >>> > >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S > >>> is in there just like before - under the organism menu there is a > >>> way to look at taxonomy...You are right, looking at this first > >>> should really help. I have made rarefaction curves of the first > >>> two samples and compared overall diversity for just the bacteria > >>> and we can discuss the results. Past is really easy so we can do > >>> more with the new samples as well. If you can get out > abundances - > >>> even just for RDP before Tuesday it would be great. > >>> > >>> Rob - One nice output of the server is a column row file of > >>> diversity (a square matrix) ready for import into software like > >>> Past. I'll pass it on to Folker! > >>> > >>> all the best, > >>> Dawn > >> > >> > >> > >> -- > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > >> Molecular Ecologist > >> Plymouth Marine Laboratory, > >> Prospect Place, The Hoe, > >> Plymouth, PL1 3DH, UK. > >> Work Tel: +44 (0)1752 633 416 > >> Home Tel: +44 (0)1752 255 783 > >> Mobile Tel: +44 (0)7764 190 147 > >> Email: gilbertjack(a)gmail.com > > > > > > > > -- > > This message (and any attachments) is for the recipient only. NERC > > is subject to the Freedom of Information Act 2000 and the contents > > of this email and any reply you make may be disclosed by NERC unless > > it is exempt from release under the Act. Any material supplied to > > NERC may be stored in an electronic records management system. > > > > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > > > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com > > > > -- > > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com > > > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com

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Re: mg-rast Re: 454 - account already made for Bergen data
by Jack Gilbert 17 Sep '07

17 Sep '07

Folker, One more thing. The taxanomic heat map....how is it constructed, what taxanomic affiliation does it use to infer relative abundance, protein BLAST hits or some kind of phylogenetic marker? Cheers Jack On 9/17/07, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > > Folker or Rob, > > Is there any reason why I might get an incomplete blast search results > page...it looks like when i search against our data it returns > nothing....even for genes that SEED suggests are found in the data. > > Link fault? > > Let me know > > jack > > > On 9/17/07, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > > > > folker, > > > > I agree with dawn, but would go further to suggest that a sequence > > identity matrix (% identity for each) for the 16S seqs from each pyroseq run > > would be a great, it would mean that we would not have to pull out > > individual 16S seqs and run this operation here. > > > > Dawn, > > > > You submitted 630 and 632 to the SEED it has been run with the new > > database, hence the 64% sequences found in the database. > > > > I have uploaded the new seqs to SEED hopefully these will be done by > > tomorrow, if not by today. > > > > re. clustering, lets talk about this tomorrow. It might give us > > something interesting and if there is a less labour intensive way of doing > > it then I would jump on it. However, it might not. There is no real link > > between what clustering tells us and the statistical analysis performed by > > Rob, which I was surprised about. anyway talk about this tomorrow. > > > > There was a small prob with the pyro run from Liverpool and so we have > > got less than an anticipated but he is re running the samples and hopefully > > will get it sorted, so should end up with more than we requested. DNA will > > be done soon as well....this is essential for the comparison between GC-20 > > and Flx...that is supposed to be done by end of this week...fingers crossed. > > > > > > I will have a word with Neil, but he is going away for a while, so will > > have to see how long it will take. > > > > folker, thank you for your help, I am keen to see what would happen when > > silva is introduced....although the short seq reads might cause F-O and > > Wolfgang some consternation! > > > > Cheers > > > > Jack > > > > > > > > > > On 9/17/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: > > > > > > Doh...forgot who I was talking to :-) Great if Silva can be > > > grabbed - do you have a timeline? > > > > > > Yes, it would be fabulous to meet up. You are more than welcome to > > > visit Oxford. We can set you up a seminar or do something more casual - > > > where will you be? > > > > > > We should get initial feedback on the river microbe proposal next week > > > and a more final decision next month - I think they will come back to PIs > > > for more information - and knowing updates to the SEED will be really > > > helpful. > > > > > > I don't know if Rob had time to debrief you from the US-EU Task force > > > but Stefan Schuster presented on MEGAN. I think he and Rob worked out a way > > > to build a plugin to the SEED that would output data ready for viewing in > > > MEGAN - just to confirm we'd be really keen on this. > > > > > > Also really keen on having on diversity matrix ( samples in columns, > > > taxa in rows, in a square matrix) produced from that taxonomy analysis but > > > perhaps downstream after sliva (as we can manually make these here) and > > > fasta files of just 16S (maybe this is already there, just haven't seen it). > > > > > > > > > Dawn > > > > > > >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> > > > Dear Dawn, > > > > > > I will send an email to Frank Oliver. > > > > > > > > > Cheers, > > > Folker > > > PS: I am planning to be in Europe some time in early November for a > > > workshop. If there is any reason to meet that would be a good time. > > > > > > On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > > > > > > > Dear Folker, > > > > > > > > I don't know if Rob has already mentioned this but we would really > > > > love to have the Silva database behind SEED for the sake of making > > > > taxonomic assignments. > > > > > > > > http://www.arb-silva.de/ > > > > > > > > It is great, the largest 16S database around now, actively > > > > developed and has all three domains. Rob thought it was a good > > > > idea too :-) > > > > > > > > If you don't already have connections, we can put you in touch with > > > > the developers if there are any issues to clarify before > > > > considering it. > > > > > > > > I assume (?) it's as simple as downloading and putting another > > > > option in the pipeline? > > > > > > > > Dawn > > > > > > > > > > > > > > > >>>> Folker Meyer < folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > > > > Jack: > > > > > > > > so ensure compatibility we did run all old metagenomes against a > > > > stable version of our internal databases. > > > > > > > > Now we updated all DBs used for analysis. The first runs were > > > > previously analyzed with a rather ancient version of our NR (non > > > > redundant protein database) and also a very old subsystem > > > collection. > > > > > > > > This explains the dramatic change. The current subsystem collection > > > > has more than 600 subsystems (old one had significantly less) and > > > > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > > > > etc... > > > > > > > > Hope that helps, > > > > Folker > > > > > > > > > > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > > > > > > > >> Rob and/or mg-rast techs. > > > >> > > > >> just looking at the sequencing data from the first 454 runs (Bag1 > > > >> and Bag6, 630 and 632) and the number of sequences that are found > > > >> within subsystem catagories has leapt from 24% to 64%.....this > > > >> seems amazing to me. > > > >> > > > >> Does this mean that SEED has suddenly expanded to include a lot > > > >> more information or is this due to a new analysis > > > >> technique...interested to know. > > > >> > > > >> Jack > > > >> > > > >> > > > >> On 9/14/07, Rob Edwards < raedwards(a)gmail.com> wrote: Jack, Dawn, > > > >> > > > >> I'm forwarding this to our internal mailing list for developers > > > that > > > >> work on the metagenomics RAST for two reasons - its great to see > > > some > > > >> praise once in a while in amongst all the people that get stuck or > > > >> have problems, and also because they can answer all the specifics > > > of > > > >> what is being done and how. > > > >> > > > >> Rob > > > >> > > > >> > > > >> > > > >> Begin forwarded message: > > > >> > > > >>> From: "Jack Gilbert" < gilbertjack(a)gmail.com> > > > >>> Date: September 14, 2007 4:51:31 AM PDT > > > >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> > > > >>> Cc: raedwards(a)gmail.com > > > >>> Subject: Re: 454 - account already made for Bergen data > > > >>> > > > >>> Dawn and Rob, > > > >>> > > > >>> I know I saw all the menus but from my end I can only see the > > > >>> diversity info for protein sequences not for rdp, green genes or > > > >> ERD. > > > >>> > > > >>> I agree the taxanomic comprison heatmap is fantastic. However, > > > what > > > >>> is used to construct it? > > > >>> > > > >>> Jack > > > >>> > > > >>> > > > >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S > > > >>> is in there just like before - under the organism menu there is a > > > >>> way to look at taxonomy...You are right, looking at this first > > > >>> should really help. I have made rarefaction curves of the first > > > >>> two samples and compared overall diversity for just the bacteria > > > >>> and we can discuss the results. Past is really easy so we can do > > > >>> more with the new samples as well. If you can get out abundances > > > - > > > >>> even just for RDP before Tuesday it would be great. > > > >>> > > > >>> Rob - One nice output of the server is a column row file of > > > >>> diversity (a square matrix) ready for import into software like > > > >>> Past. I'll pass it on to Folker! > > > >>> > > > >>> all the best, > > > >>> Dawn > > > >> > > > >> > > > >> > > > >> -- > > > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > > > >> Molecular Ecologist > > > >> Plymouth Marine Laboratory, > > > >> Prospect Place, The Hoe, > > > >> Plymouth, PL1 3DH, UK. > > > >> Work Tel: +44 (0)1752 633 416 > > > >> Home Tel: +44 (0)1752 255 783 > > > >> Mobile Tel: +44 (0)7764 190 147 > > > >> Email: gilbertjack(a)gmail.com > > > > > > > > > > > > > > > > -- > > > > This message (and any attachments) is for the recipient only. NERC > > > > is subject to the Freedom of Information Act 2000 and the contents > > > > of this email and any reply you make may be disclosed by NERC unless > > > > it is exempt from release under the Act. Any material supplied to > > > > NERC may be stored in an electronic records management system. > > > > > > > > > > > > > -- > > > This message (and any attachments) is for the recipient only. NERC > > > is subject to the Freedom of Information Act 2000 and the contents > > > of this email and any reply you make may be disclosed by NERC unless > > > it is exempt from release under the Act. Any material supplied to > > > NERC may be stored in an electronic records management system. > > > > > > > > > > > > -- > > Dr. Jack A. Gilbert B.Sc. Ph.D. > > Molecular Ecologist > > Plymouth Marine Laboratory, > > Prospect Place, The Hoe, > > Plymouth, PL1 3DH, UK. > > Work Tel: +44 (0)1752 633 416 > > Home Tel: +44 (0)1752 255 783 > > Mobile Tel: +44 (0)7764 190 147 > > Email: gilbertjack(a)gmail.com > > > > > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: gilbertjack(a)gmail.com

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Re: mg-rast Re: 454 - account already made for Bergen data
by Jack Gilbert 17 Sep '07

17 Sep '07

Folker or Rob, Is there any reason why I might get an incomplete blast search results page...it looks like when i search against our data it returns nothing....even for genes that SEED suggests are found in the data. Link fault? Let me know jack On 9/17/07, Jack Gilbert <gilbertjack(a)gmail.com> wrote: > > folker, > > I agree with dawn, but would go further to suggest that a sequence > identity matrix (% identity for each) for the 16S seqs from each pyroseq run > would be a great, it would mean that we would not have to pull out > individual 16S seqs and run this operation here. > > Dawn, > > You submitted 630 and 632 to the SEED it has been run with the new > database, hence the 64% sequences found in the database. > > I have uploaded the new seqs to SEED hopefully these will be done by > tomorrow, if not by today. > > re. clustering, lets talk about this tomorrow. It might give us something > interesting and if there is a less labour intensive way of doing it then I > would jump on it. However, it might not. There is no real link between what > clustering tells us and the statistical analysis performed by Rob, which I > was surprised about. anyway talk about this tomorrow. > > There was a small prob with the pyro run from Liverpool and so we have got > less than an anticipated but he is re running the samples and hopefully will > get it sorted, so should end up with more than we requested. DNA will be > done soon as well....this is essential for the comparison between GC-20 and > Flx...that is supposed to be done by end of this week...fingers crossed. > > I will have a word with Neil, but he is going away for a while, so will > have to see how long it will take. > > folker, thank you for your help, I am keen to see what would happen when > silva is introduced....although the short seq reads might cause F-O and > Wolfgang some consternation! > > Cheers > > Jack > > > > > On 9/17/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: > > > > Doh...forgot who I was talking to :-) Great if Silva can be grabbed - > > do you have a timeline? > > > > Yes, it would be fabulous to meet up. You are more than welcome to > > visit Oxford. We can set you up a seminar or do something more casual - > > where will you be? > > > > We should get initial feedback on the river microbe proposal next week > > and a more final decision next month - I think they will come back to PIs > > for more information - and knowing updates to the SEED will be really > > helpful. > > > > I don't know if Rob had time to debrief you from the US-EU Task force > > but Stefan Schuster presented on MEGAN. I think he and Rob worked out a way > > to build a plugin to the SEED that would output data ready for viewing in > > MEGAN - just to confirm we'd be really keen on this. > > > > Also really keen on having on diversity matrix ( samples in columns, > > taxa in rows, in a square matrix) produced from that taxonomy analysis but > > perhaps downstream after sliva (as we can manually make these here) and > > fasta files of just 16S (maybe this is already there, just haven't seen it). > > > > > > Dawn > > > > >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> > > Dear Dawn, > > > > I will send an email to Frank Oliver. > > > > > > Cheers, > > Folker > > PS: I am planning to be in Europe some time in early November for a > > workshop. If there is any reason to meet that would be a good time. > > > > On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > > > > > Dear Folker, > > > > > > I don't know if Rob has already mentioned this but we would really > > > love to have the Silva database behind SEED for the sake of making > > > taxonomic assignments. > > > > > > http://www.arb-silva.de/ > > > > > > It is great, the largest 16S database around now, actively > > > developed and has all three domains. Rob thought it was a good > > > idea too :-) > > > > > > If you don't already have connections, we can put you in touch with > > > the developers if there are any issues to clarify before > > > considering it. > > > > > > I assume (?) it's as simple as downloading and putting another > > > option in the pipeline? > > > > > > Dawn > > > > > > > > > > > >>>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > > > Jack: > > > > > > so ensure compatibility we did run all old metagenomes against a > > > stable version of our internal databases. > > > > > > Now we updated all DBs used for analysis. The first runs were > > > previously analyzed with a rather ancient version of our NR (non > > > redundant protein database) and also a very old subsystem collection. > > > > > > This explains the dramatic change. The current subsystem collection > > > has more than 600 subsystems (old one had significantly less) and > > > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > > > etc... > > > > > > Hope that helps, > > > Folker > > > > > > > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > > > > > >> Rob and/or mg-rast techs. > > >> > > >> just looking at the sequencing data from the first 454 runs (Bag1 > > >> and Bag6, 630 and 632) and the number of sequences that are found > > >> within subsystem catagories has leapt from 24% to 64%.....this > > >> seems amazing to me. > > >> > > >> Does this mean that SEED has suddenly expanded to include a lot > > >> more information or is this due to a new analysis > > >> technique...interested to know. > > >> > > >> Jack > > >> > > >> > > >> On 9/14/07, Rob Edwards < raedwards(a)gmail.com> wrote: Jack, Dawn, > > >> > > >> I'm forwarding this to our internal mailing list for developers that > > >> work on the metagenomics RAST for two reasons - its great to see some > > > > >> praise once in a while in amongst all the people that get stuck or > > >> have problems, and also because they can answer all the specifics of > > >> what is being done and how. > > >> > > >> Rob > > >> > > >> > > >> > > >> Begin forwarded message: > > >> > > >>> From: "Jack Gilbert" <gilbertjack(a)gmail.com> > > >>> Date: September 14, 2007 4:51:31 AM PDT > > >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> > > >>> Cc: raedwards(a)gmail.com > > >>> Subject: Re: 454 - account already made for Bergen data > > >>> > > >>> Dawn and Rob, > > >>> > > >>> I know I saw all the menus but from my end I can only see the > > >>> diversity info for protein sequences not for rdp, green genes or > > >> ERD. > > >>> > > >>> I agree the taxanomic comprison heatmap is fantastic. However, what > > >>> is used to construct it? > > >>> > > >>> Jack > > >>> > > >>> > > >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S > > >>> is in there just like before - under the organism menu there is a > > >>> way to look at taxonomy...You are right, looking at this first > > >>> should really help. I have made rarefaction curves of the first > > >>> two samples and compared overall diversity for just the bacteria > > >>> and we can discuss the results. Past is really easy so we can do > > >>> more with the new samples as well. If you can get out abundances - > > >>> even just for RDP before Tuesday it would be great. > > >>> > > >>> Rob - One nice output of the server is a column row file of > > >>> diversity (a square matrix) ready for import into software like > > >>> Past. I'll pass it on to Folker! > > >>> > > >>> all the best, > > >>> Dawn > > >> > > >> > > >> > > >> -- > > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > > >> Molecular Ecologist > > >> Plymouth Marine Laboratory, > > >> Prospect Place, The Hoe, > > >> Plymouth, PL1 3DH, UK. > > >> Work Tel: +44 (0)1752 633 416 > > >> Home Tel: +44 (0)1752 255 783 > > >> Mobile Tel: +44 (0)7764 190 147 > > >> Email: gilbertjack(a)gmail.com > > > > > > > > > > > > -- > > > This message (and any attachments) is for the recipient only. NERC > > > is subject to the Freedom of Information Act 2000 and the contents > > > of this email and any reply you make may be disclosed by NERC unless > > > it is exempt from release under the Act. Any material supplied to > > > NERC may be stored in an electronic records management system. > > > > > > > > > -- > > This message (and any attachments) is for the recipient only. NERC > > is subject to the Freedom of Information Act 2000 and the contents > > of this email and any reply you make may be disclosed by NERC unless > > it is exempt from release under the Act. Any material supplied to > > NERC may be stored in an electronic records management system. > > > > > > > -- > Dr. Jack A. Gilbert B.Sc. Ph.D. > Molecular Ecologist > Plymouth Marine Laboratory, > Prospect Place, The Hoe, > Plymouth, PL1 3DH, UK. > Work Tel: +44 (0)1752 633 416 > Home Tel: +44 (0)1752 255 783 > Mobile Tel: +44 (0)7764 190 147 > Email: gilbertjack(a)gmail.com > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: gilbertjack(a)gmail.com

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mg-rast getting silva into SEED - etc
by Dawn Field 17 Sep '07

17 Sep '07

Jack Yes, one matrix with a number of hits per taxa per staff AND information on best hit as it contains a lot of information for biological interpretation. Looking at these current list I don't know if it's is an exact match to a particular 16S or a 'best match' and if the later what percentage difference (given that 3% is a species' and 10% a family.) From the later we can get at the amount of novel diversity in the dataset etc. If we get the fasta file - or better something integrated with a selected tree - perhaps something from silva?? - it would be a fabulous addition to SEED and a huge help to us (yes, I agree about the short read issue too - but the new datasets are >200bp). Jack - for example, we have 'unclassified' under greengenes and european ribosomal database but it would be fabulous to know if they are all relatively similar sequences (1 abundant lineage) and very different (many different lineages) best, Dawn >>> "Jack Gilbert" <gilbertjack(a)gmail.com> 9/17/07 15:05 >>> folker, I agree with dawn, but would go further to suggest that a sequence identity matrix (% identity for each) for the 16S seqs from each pyroseq run would be a great, it would mean that we would not have to pull out individual 16S seqs and run this operation here. Dawn, You submitted 630 and 632 to the SEED it has been run with the new database, hence the 64% sequences found in the database. I have uploaded the new seqs to SEED hopefully these will be done by tomorrow, if not by today. re. clustering, lets talk about this tomorrow. It might give us something interesting and if there is a less labour intensive way of doing it then I would jump on it. However, it might not. There is no real link between what clustering tells us and the statistical analysis performed by Rob, which I was surprised about. anyway talk about this tomorrow. There was a small prob with the pyro run from Liverpool and so we have got less than an anticipated but he is re running the samples and hopefully will get it sorted, so should end up with more than we requested. DNA will be done soon as well....this is essential for the comparison between GC-20 and Flx...that is supposed to be done by end of this week...fingers crossed. I will have a word with Neil, but he is going away for a while, so will have to see how long it will take. folker, thank you for your help, I am keen to see what would happen when silva is introduced....although the short seq reads might cause F-O and Wolfgang some consternation! Cheers Jack On 9/17/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: > > Doh...forgot who I was talking to :-) Great if Silva can be grabbed - do > you have a timeline? > > Yes, it would be fabulous to meet up. You are more than welcome to visit > Oxford. We can set you up a seminar or do something more casual - where > will you be? > > We should get initial feedback on the river microbe proposal next week and > a more final decision next month - I think they will come back to PIs for > more information - and knowing updates to the SEED will be really helpful. > > I don't know if Rob had time to debrief you from the US-EU Task force but > Stefan Schuster presented on MEGAN. I think he and Rob worked out a way to > build a plugin to the SEED that would output data ready for viewing in MEGAN > - just to confirm we'd be really keen on this. > > Also really keen on having on diversity matrix ( samples in columns, taxa > in rows, in a square matrix) produced from that taxonomy analysis but > perhaps downstream after sliva (as we can manually make these here) and > fasta files of just 16S (maybe this is already there, just haven't seen it). > > Dawn > > >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> > Dear Dawn, > > I will send an email to Frank Oliver. > > > Cheers, > Folker > PS: I am planning to be in Europe some time in early November for a > workshop. If there is any reason to meet that would be a good time. > > On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > > > Dear Folker, > > > > I don't know if Rob has already mentioned this but we would really > > love to have the Silva database behind SEED for the sake of making > > taxonomic assignments. > > > > http://www.arb-silva.de/ > > > > It is great, the largest 16S database around now, actively > > developed and has all three domains. Rob thought it was a good > > idea too :-) > > > > If you don't already have connections, we can put you in touch with > > the developers if there are any issues to clarify before > > considering it. > > > > I assume (?) it's as simple as downloading and putting another > > option in the pipeline? > > > > Dawn > > > > > > > >>>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > > Jack: > > > > so ensure compatibility we did run all old metagenomes against a > > stable version of our internal databases. > > > > Now we updated all DBs used for analysis. The first runs were > > previously analyzed with a rather ancient version of our NR (non > > redundant protein database) and also a very old subsystem collection. > > > > This explains the dramatic change. The current subsystem collection > > has more than 600 subsystems (old one had significantly less) and > > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > > etc... > > > > Hope that helps, > > Folker > > > > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > > > >> Rob and/or mg-rast techs. > >> > >> just looking at the sequencing data from the first 454 runs (Bag1 > >> and Bag6, 630 and 632) and the number of sequences that are found > >> within subsystem catagories has leapt from 24% to 64%.....this > >> seems amazing to me. > >> > >> Does this mean that SEED has suddenly expanded to include a lot > >> more information or is this due to a new analysis > >> technique...interested to know. > >> > >> Jack > >> > >> > >> On 9/14/07, Rob Edwards <raedwards(a)gmail.com> wrote: Jack, Dawn, > >> > >> I'm forwarding this to our internal mailing list for developers that > >> work on the metagenomics RAST for two reasons - its great to see some > >> praise once in a while in amongst all the people that get stuck or > >> have problems, and also because they can answer all the specifics of > >> what is being done and how. > >> > >> Rob > >> > >> > >> > >> Begin forwarded message: > >> > >>> From: "Jack Gilbert" <gilbertjack(a)gmail.com> > >>> Date: September 14, 2007 4:51:31 AM PDT > >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> > >>> Cc: raedwards(a)gmail.com > >>> Subject: Re: 454 - account already made for Bergen data > >>> > >>> Dawn and Rob, > >>> > >>> I know I saw all the menus but from my end I can only see the > >>> diversity info for protein sequences not for rdp, green genes or > >> ERD. > >>> > >>> I agree the taxanomic comprison heatmap is fantastic. However, what > >>> is used to construct it? > >>> > >>> Jack > >>> > >>> > >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S > >>> is in there just like before - under the organism menu there is a > >>> way to look at taxonomy...You are right, looking at this first > >>> should really help. I have made rarefaction curves of the first > >>> two samples and compared overall diversity for just the bacteria > >>> and we can discuss the results. Past is really easy so we can do > >>> more with the new samples as well. If you can get out abundances - > >>> even just for RDP before Tuesday it would be great. > >>> > >>> Rob - One nice output of the server is a column row file of > >>> diversity (a square matrix) ready for import into software like > >>> Past. I'll pass it on to Folker! > >>> > >>> all the best, > >>> Dawn > >> > >> > >> > >> -- > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > >> Molecular Ecologist > >> Plymouth Marine Laboratory, > >> Prospect Place, The Hoe, > >> Plymouth, PL1 3DH, UK. > >> Work Tel: +44 (0)1752 633 416 > >> Home Tel: +44 (0)1752 255 783 > >> Mobile Tel: +44 (0)7764 190 147 > >> Email: gilbertjack(a)gmail.com > > > > > > > > -- > > This message (and any attachments) is for the recipient only. NERC > > is subject to the Freedom of Information Act 2000 and the contents > > of this email and any reply you make may be disclosed by NERC unless > > it is exempt from release under the Act. Any material supplied to > > NERC may be stored in an electronic records management system. > > > > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: gilbertjack(a)gmail.com -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.

1 0

Re: mg-rast Re: 454 - account already made for Bergen data
by Jack Gilbert 17 Sep '07

17 Sep '07

folker, I agree with dawn, but would go further to suggest that a sequence identity matrix (% identity for each) for the 16S seqs from each pyroseq run would be a great, it would mean that we would not have to pull out individual 16S seqs and run this operation here. Dawn, You submitted 630 and 632 to the SEED it has been run with the new database, hence the 64% sequences found in the database. I have uploaded the new seqs to SEED hopefully these will be done by tomorrow, if not by today. re. clustering, lets talk about this tomorrow. It might give us something interesting and if there is a less labour intensive way of doing it then I would jump on it. However, it might not. There is no real link between what clustering tells us and the statistical analysis performed by Rob, which I was surprised about. anyway talk about this tomorrow. There was a small prob with the pyro run from Liverpool and so we have got less than an anticipated but he is re running the samples and hopefully will get it sorted, so should end up with more than we requested. DNA will be done soon as well....this is essential for the comparison between GC-20 and Flx...that is supposed to be done by end of this week...fingers crossed. I will have a word with Neil, but he is going away for a while, so will have to see how long it will take. folker, thank you for your help, I am keen to see what would happen when silva is introduced....although the short seq reads might cause F-O and Wolfgang some consternation! Cheers Jack On 9/17/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: > > Doh...forgot who I was talking to :-) Great if Silva can be grabbed - do > you have a timeline? > > Yes, it would be fabulous to meet up. You are more than welcome to visit > Oxford. We can set you up a seminar or do something more casual - where > will you be? > > We should get initial feedback on the river microbe proposal next week and > a more final decision next month - I think they will come back to PIs for > more information - and knowing updates to the SEED will be really helpful. > > I don't know if Rob had time to debrief you from the US-EU Task force but > Stefan Schuster presented on MEGAN. I think he and Rob worked out a way to > build a plugin to the SEED that would output data ready for viewing in MEGAN > - just to confirm we'd be really keen on this. > > Also really keen on having on diversity matrix ( samples in columns, taxa > in rows, in a square matrix) produced from that taxonomy analysis but > perhaps downstream after sliva (as we can manually make these here) and > fasta files of just 16S (maybe this is already there, just haven't seen it). > > Dawn > > >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> > Dear Dawn, > > I will send an email to Frank Oliver. > > > Cheers, > Folker > PS: I am planning to be in Europe some time in early November for a > workshop. If there is any reason to meet that would be a good time. > > On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > > > Dear Folker, > > > > I don't know if Rob has already mentioned this but we would really > > love to have the Silva database behind SEED for the sake of making > > taxonomic assignments. > > > > http://www.arb-silva.de/ > > > > It is great, the largest 16S database around now, actively > > developed and has all three domains. Rob thought it was a good > > idea too :-) > > > > If you don't already have connections, we can put you in touch with > > the developers if there are any issues to clarify before > > considering it. > > > > I assume (?) it's as simple as downloading and putting another > > option in the pipeline? > > > > Dawn > > > > > > > >>>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > > Jack: > > > > so ensure compatibility we did run all old metagenomes against a > > stable version of our internal databases. > > > > Now we updated all DBs used for analysis. The first runs were > > previously analyzed with a rather ancient version of our NR (non > > redundant protein database) and also a very old subsystem collection. > > > > This explains the dramatic change. The current subsystem collection > > has more than 600 subsystems (old one had significantly less) and > > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > > etc... > > > > Hope that helps, > > Folker > > > > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > > > >> Rob and/or mg-rast techs. > >> > >> just looking at the sequencing data from the first 454 runs (Bag1 > >> and Bag6, 630 and 632) and the number of sequences that are found > >> within subsystem catagories has leapt from 24% to 64%.....this > >> seems amazing to me. > >> > >> Does this mean that SEED has suddenly expanded to include a lot > >> more information or is this due to a new analysis > >> technique...interested to know. > >> > >> Jack > >> > >> > >> On 9/14/07, Rob Edwards <raedwards(a)gmail.com> wrote: Jack, Dawn, > >> > >> I'm forwarding this to our internal mailing list for developers that > >> work on the metagenomics RAST for two reasons - its great to see some > >> praise once in a while in amongst all the people that get stuck or > >> have problems, and also because they can answer all the specifics of > >> what is being done and how. > >> > >> Rob > >> > >> > >> > >> Begin forwarded message: > >> > >>> From: "Jack Gilbert" <gilbertjack(a)gmail.com> > >>> Date: September 14, 2007 4:51:31 AM PDT > >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> > >>> Cc: raedwards(a)gmail.com > >>> Subject: Re: 454 - account already made for Bergen data > >>> > >>> Dawn and Rob, > >>> > >>> I know I saw all the menus but from my end I can only see the > >>> diversity info for protein sequences not for rdp, green genes or > >> ERD. > >>> > >>> I agree the taxanomic comprison heatmap is fantastic. However, what > >>> is used to construct it? > >>> > >>> Jack > >>> > >>> > >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S > >>> is in there just like before - under the organism menu there is a > >>> way to look at taxonomy...You are right, looking at this first > >>> should really help. I have made rarefaction curves of the first > >>> two samples and compared overall diversity for just the bacteria > >>> and we can discuss the results. Past is really easy so we can do > >>> more with the new samples as well. If you can get out abundances - > >>> even just for RDP before Tuesday it would be great. > >>> > >>> Rob - One nice output of the server is a column row file of > >>> diversity (a square matrix) ready for import into software like > >>> Past. I'll pass it on to Folker! > >>> > >>> all the best, > >>> Dawn > >> > >> > >> > >> -- > >> Dr. Jack A. Gilbert B.Sc. Ph.D. > >> Molecular Ecologist > >> Plymouth Marine Laboratory, > >> Prospect Place, The Hoe, > >> Plymouth, PL1 3DH, UK. > >> Work Tel: +44 (0)1752 633 416 > >> Home Tel: +44 (0)1752 255 783 > >> Mobile Tel: +44 (0)7764 190 147 > >> Email: gilbertjack(a)gmail.com > > > > > > > > -- > > This message (and any attachments) is for the recipient only. NERC > > is subject to the Freedom of Information Act 2000 and the contents > > of this email and any reply you make may be disclosed by NERC unless > > it is exempt from release under the Act. Any material supplied to > > NERC may be stored in an electronic records management system. > > > > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > > -- Dr. Jack A. Gilbert B.Sc. Ph.D. Molecular Ecologist Plymouth Marine Laboratory, Prospect Place, The Hoe, Plymouth, PL1 3DH, UK. Work Tel: +44 (0)1752 633 416 Home Tel: +44 (0)1752 255 783 Mobile Tel: +44 (0)7764 190 147 Email: gilbertjack(a)gmail.com

1 0

Re: mg-rast Re: 454 - account already made for Bergen data
by Dawn Field 17 Sep '07

17 Sep '07

Doh...forgot who I was talking to :-) Great if Silva can be grabbed - do you have a timeline? Yes, it would be fabulous to meet up. You are more than welcome to visit Oxford. We can set you up a seminar or do something more casual - where will you be? We should get initial feedback on the river microbe proposal next week and a more final decision next month - I think they will come back to PIs for more information - and knowing updates to the SEED will be really helpful. I don't know if Rob had time to debrief you from the US-EU Task force but Stefan Schuster presented on MEGAN. I think he and Rob worked out a way to build a plugin to the SEED that would output data ready for viewing in MEGAN - just to confirm we'd be really keen on this. Also really keen on having on diversity matrix ( samples in columns, taxa in rows, in a square matrix) produced from that taxonomy analysis but perhaps downstream after sliva (as we can manually make these here) and fasta files of just 16S (maybe this is already there, just haven't seen it). Dawn >>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 14:28 >>> Dear Dawn, I will send an email to Frank Oliver. Cheers, Folker PS: I am planning to be in Europe some time in early November for a workshop. If there is any reason to meet that would be a good time. On Sep 17, 2007, at 8:13 AM, Dawn Field wrote: > Dear Folker, > > I don't know if Rob has already mentioned this but we would really > love to have the Silva database behind SEED for the sake of making > taxonomic assignments. > > http://www.arb-silva.de/ > > It is great, the largest 16S database around now, actively > developed and has all three domains. Rob thought it was a good > idea too :-) > > If you don't already have connections, we can put you in touch with > the developers if there are any issues to clarify before > considering it. > > I assume (?) it's as simple as downloading and putting another > option in the pipeline? > > Dawn > > > >>>> Folker Meyer <folker(a)mcs.anl.gov> 9/17/07 12:21 >>> > Jack: > > so ensure compatibility we did run all old metagenomes against a > stable version of our internal databases. > > Now we updated all DBs used for analysis. The first runs were > previously analyzed with a rather ancient version of our NR (non > redundant protein database) and also a very old subsystem collection. > > This explains the dramatic change. The current subsystem collection > has more than 600 subsystems (old one had significantly less) and > covers approx. 40-50% of all proteins in Strep., Staph, or Ecoli > etc... > > Hope that helps, > Folker > > > On Sep 17, 2007, at 5:51 AM, Jack Gilbert wrote: > >> Rob and/or mg-rast techs. >> >> just looking at the sequencing data from the first 454 runs (Bag1 >> and Bag6, 630 and 632) and the number of sequences that are found >> within subsystem catagories has leapt from 24% to 64%.....this >> seems amazing to me. >> >> Does this mean that SEED has suddenly expanded to include a lot >> more information or is this due to a new analysis >> technique...interested to know. >> >> Jack >> >> >> On 9/14/07, Rob Edwards <raedwards(a)gmail.com> wrote: Jack, Dawn, >> >> I'm forwarding this to our internal mailing list for developers that >> work on the metagenomics RAST for two reasons - its great to see some >> praise once in a while in amongst all the people that get stuck or >> have problems, and also because they can answer all the specifics of >> what is being done and how. >> >> Rob >> >> >> >> Begin forwarded message: >> >>> From: "Jack Gilbert" <gilbertjack(a)gmail.com> >>> Date: September 14, 2007 4:51:31 AM PDT >>> To: "Dawn Field" < dfield(a)ceh.ac.uk> >>> Cc: raedwards(a)gmail.com >>> Subject: Re: 454 - account already made for Bergen data >>> >>> Dawn and Rob, >>> >>> I know I saw all the menus but from my end I can only see the >>> diversity info for protein sequences not for rdp, green genes or >> ERD. >>> >>> I agree the taxanomic comprison heatmap is fantastic. However, what >>> is used to construct it? >>> >>> Jack >>> >>> >>> On 9/14/07, Dawn Field <dfield(a)ceh.ac.uk> wrote: Hi Jack! The 16S >>> is in there just like before - under the organism menu there is a >>> way to look at taxonomy...You are right, looking at this first >>> should really help. I have made rarefaction curves of the first >>> two samples and compared overall diversity for just the bacteria >>> and we can discuss the results. Past is really easy so we can do >>> more with the new samples as well. If you can get out abundances - >>> even just for RDP before Tuesday it would be great. >>> >>> Rob - One nice output of the server is a column row file of >>> diversity (a square matrix) ready for import into software like >>> Past. I'll pass it on to Folker! >>> >>> all the best, >>> Dawn >> >> >> >> -- >> Dr. Jack A. Gilbert B.Sc. Ph.D. >> Molecular Ecologist >> Plymouth Marine Laboratory, >> Prospect Place, The Hoe, >> Plymouth, PL1 3DH, UK. >> Work Tel: +44 (0)1752 633 416 >> Home Tel: +44 (0)1752 255 783 >> Mobile Tel: +44 (0)7764 190 147 >> Email: gilbertjack(a)gmail.com > > > > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.

1 0