October 2010 - Mg-rast - mailman3.cels.anl.gov

Re: [mg-rast] Fwd: [theseed.org Info] Query with seed results
by Folker Meyer 31 Oct '10

31 Oct '10

Manisha: the algorithms used by Jim Knights GS-Mapper software and blast used are vastly different. Also: mapping against a database of just one organisms will yield different results. In addition what cut-offs were used in the gs-mapper and in the BLAST output from MG-RAST? Best, Folker Meyer On Oct 28, 2010, at 7:41 AM, Robert Olson wrote: > FYI > > ----- Forwarded Message ----- > From: "Manisha Sajnani" <mani.sajnani(a)gmail.com> > To: info(a)theseed.org > Sent: Thursday, October 28, 2010 12:59:49 AM GMT -06:00 US/Canada Central > Subject: Re: [theseed.org Info] Query with seed results > > > Dear Sir > > > Currently we have submitted sequences at MGRAST server with Job: 11673 and ID:4451984.3. According to the MGRAST phylogenetic seed analysis shows following results: > > > > > > > Organism > > Hits > > % identity > > > Acidiphilium cryptum JF-5 > > 66 > > 4.517% > > > Thiobacillus denitrificans ATCC 25259 > > 63 > > 4.312% > > > Acidithiobacillus ferrooxidans ATCC 23270 > > 8 > > > > 0.548% > > > > Simuntaneously we have mapped/aligned our sequences with Acidithiobacillus ferrooxidans ATCC 23270 using 454 GS Mapper tool and we are getting 81.61% match. > > > > > Organism > > Hits > > % identity > > > Acidithiobacillus ferrooxidans ATCC 23270 > > 923 > > > > 81.61% > > Acidithiobacillus ferrooxidans ATCC 23270 genome has been downloaded from ncbi site and mapped to our tool. Kindly inform us why is such a big difference in the results > > > Regards > Manisha Sajnani > Animal Biotechnology > Anand Agricultural University > Anand 390010. > India > _______________________________________________ > Info mailing list > Info(a)lists.theseed.org > https://lists.theseed.org/mailman/listinfo/info

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Re: [mg-rast] turn around re: 11775
by Folker Meyer 31 Oct '10

31 Oct '10

Ryan: be deleting and resubmitting you have given up your position in the queue. The queue is about 10GB, to it will be approx 10 days. It would have been another 1-2 days before. Best, Folker On Oct 27, 2010, at 6:46 PM, Ryan Lynch wrote: > Hey guys, > Just curious what the ball park time is to finish jobs submitted to mg rast currently. > > I submitted a 239698813 bp job and it sat at step 4 for a week, so I deleted and resubmitted, and it's been there for a day or so. > > Thanks, > Ryan Lynch > > mg rast user: rlynch > job id: 11775

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Re: [mg-rast] Query
by Folker Meyer 29 Oct '10

29 Oct '10

Dear Vaibhav Bhatt the system currently has about 10GB in the queue and will take a few more days to process. best, Folker On Oct 28, 2010, at 10:49 PM, vaibhav bhatt wrote: > Dear Sir/Mam, > I have a query that, i have uploaded three files in MG-RAST (job no 11628, 11629 and 11672) for analysis, MG-RAST gives result of two files but it takes lots of time to analyze third file (job 11672, ID 4451983.3), Please let me know what is the problem, does it have any problem with my file or anything else?? I have uploaded the file on 20-10-2010 (8-9days ago). > > Thank you > > Regards > Vaibhav Bhatt > >

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sharing metagenomes
by liz dinsdale 29 Oct '10

29 Oct '10

Hi I would like to share one of my metagenomes that was up loaded by another person - is that possible the metagenome is #444511.3 or # 4435 MillSharkLIMic20090422 - up loaded by Bahador Nosrat i would like the metagenomes shared with steven.quistad(a)gmail.com thanks liz Elizabeth Dinsdale, PhD Assistant Professor Biology Department San Diego State University 5500 Campanile Dr San Diego 92182 California

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Re: [mg-rast] question on the taxonomy classification based on metabolic profile
by Folker Meyer 29 Oct '10

29 Oct '10

On Oct 29, 2010, at 11:16 AM, Liang.Zhanbei(a)epamail.epa.gov wrote: > Dear Sirs/Madams: > Thank you so much for the MG-RAST server, This is a very useful database to analysis the large number of 454 sequencing data. I have one question: since our 454 sequencing data do not contain enough 16SrRNA sequences, we have to make some phylum-level taxonomic assignment using the metabolic profiling of the sequence, Could you please show me how to do that? Do I need to use the SEED server or just use the MG-RAST server? I already have account and have my data uploaded and analysis in the MG-RAST server. Thank you again for your help. Dear Zhanbei, you can do this with the MG-RAST server. In the overview page, select Metagenome -> Sequence Profile (in the green menu bar) Once on that page, select Phylogenetic profile (as shown below). Best, Folker > > > Best regards > John > > Zhanbei (John) Liang, Ph.D > Ground Water Ecosystems Restoration Division > National Risk Management Research Laboratory > U.S. Environmental Protection Agency > 919 Kerr Lab Road > Ada, OK, 74820 > Tel: 580-436-8500 ext 8536 > Liang.Zhanbei(a)epa.gov

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question on the taxonomy classification based on metabolic profile
by Liang.Zhanbei＠epamail.epa.gov 29 Oct '10

29 Oct '10

Dear Sirs/Madams: Thank you so much for the MG-RAST server, This is a very useful database to analysis the large number of 454 sequencing data. I have one question: since our 454 sequencing data do not contain enough 16SrRNA sequences, we have to make some phylum-level taxonomic assignment using the metabolic profiling of the sequence, Could you please show me how to do that? Do I need to use the SEED server or just use the MG-RAST server? I already have account and have my data uploaded and analysis in the MG-RAST server. Thank you again for your help. Best regards John Zhanbei (John) Liang, Ph.D Ground Water Ecosystems Restoration Division National Risk Management Research Laboratory U.S. Environmental Protection Agency 919 Kerr Lab Road Ada, OK, 74820 Tel: 580-436-8500 ext 8536 Liang.Zhanbei(a)epa.gov

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Query
by vaibhav bhatt 28 Oct '10

28 Oct '10

Dear Sir/Mam, I have a query that, i have uploaded three files in MG-RAST (job no 11628, 11629 and 11672) for analysis, MG-RAST gives result of two files but it takes lots of time to analyze third file (job 11672, ID 4451983.3), Please let me know what is the problem, does it have any problem with my file or anything else?? I have uploaded the file on 20-10-2010 (8-9days ago). Thank you Regards Vaibhav Bhatt

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(Job 5019 , ID 4445106.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 28 Oct '10

28 Oct '10

Sarah Kyker (WebServerBackend::User=HASH(0x11556a10)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4445106.3.

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(Job 5043 , ID 4445130.3) . is now publicly available.
by mg-rast＠mcs.anl.gov 28 Oct '10

28 Oct '10

Sarah Kyker (WebServerBackend::User=HASH(0xc91d9f0)) has made the genome public. Link provided: http://mg-rast.mcs.anl.gov/mg-rast/FIG/linkin.cgi?metagenome=4445130.3.

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Fwd: [theseed.org Info] Query with seed results
by Robert Olson 28 Oct '10

28 Oct '10

FYI ----- Forwarded Message ----- From: "Manisha Sajnani" <mani.sajnani(a)gmail.com> To: info(a)theseed.org Sent: Thursday, October 28, 2010 12:59:49 AM GMT -06:00 US/Canada Central Subject: Re: [theseed.org Info] Query with seed results Dear Sir Currently we have submitted sequences at MGRAST server with Job: 11673 and ID:4451984.3. According to the MGRAST phylogenetic seed analysis shows following results: Organism Hits % identity Acidiphilium cryptum JF-5 66 4.517% Thiobacillus denitrificans ATCC 25259 63 4.312% Acidithiobacillus ferrooxidans ATCC 23270 8 0.548% Simuntaneously we have mapped/aligned our sequences with Acidithiobacillus ferrooxidans ATCC 23270 using 454 GS Mapper tool and we are getting 81.61% match. Organism Hits % identity Acidithiobacillus ferrooxidans ATCC 23270 923 81.61% Acidithiobacillus ferrooxidans ATCC 23270 genome has been downloaded from ncbi site and mapped to our tool. Kindly inform us why is such a big difference in the results Regards Manisha Sajnani Animal Biotechnology Anand Agricultural University Anand 390010. India _______________________________________________ Info mailing list Info(a)lists.theseed.org https://lists.theseed.org/mailman/listinfo/info

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