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Old 04-10-2011, 02:46 PM   #1
Chuckytah
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Question Taxonomy classifier

Hello,

I have found this website: http://rdp.cme.msu.edu/classifier/classifier.jsp but it's for bacteria and archeobacteria...

don't know about one for all the kingdoms?

I have a contigs.fasta and i want to know how many sequences i have from wich taxonomic groups...
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Old 04-10-2011, 05:00 PM   #2
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Greengenes at Lawrence Livermore will help you with that, in concert with ARB.
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Old 04-11-2011, 06:11 AM   #3
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Quote:
Originally Posted by bckirkup View Post
Greengenes at Lawrence Livermore will help you with that, in concert with ARB.

there is some website? thank you so much.

Greengenes + ARB?
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Old 04-11-2011, 06:45 AM   #4
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I think he means this website;

http://greengenes.lbl.gov/cgi-bin/nph-index.cgi
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Old 04-11-2011, 07:07 AM   #5
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thank you. Someone advised me to use MEGAN... what you think?
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Old 04-11-2011, 07:16 AM   #6
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I'd also check out Silva http://www.arb-silva.de/ it's from the guys who made Arb. The plus points are that the alignment is better than greengenes (which uses an old alignment from the Silva group) or RDP (which doesn't bother aligning the variable regions of 16S), the negative points are that aligning more than 300 sequences requires paying for their SINA aligner. You can get round this by aligning using Mothur from Pat Schloss http://www.mothur.org/, doing the alignment there and then merging it with the current Silva database.

You mention that you have a contigs file, which suggests that you're looking at metagenomics data, so perhaps you want to try something like MG RAST http://metagenomics.anl.gov/ or PhylOTU http://www.ploscompbiol.org/article/...l.pcbi.1001061 which will get you phylogenetic information from a metagenomic rather than 16S dataset?
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Old 04-11-2011, 07:20 AM   #7
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Sorry, just spotted your update. MEGAN would do the job, but check out that PhylOTU paper for a brief discussion of its limitations.
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Old 04-11-2011, 08:45 AM   #8
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Quote:
Originally Posted by Palecomic View Post
I'd also check out Silva http://www.arb-silva.de/ it's from the guys who made Arb. The plus points are that the alignment is better than greengenes (which uses an old alignment from the Silva group) or RDP (which doesn't bother aligning the variable regions of 16S), the negative points are that aligning more than 300 sequences requires paying for their SINA aligner. You can get round this by aligning using Mothur from Pat Schloss http://www.mothur.org/, doing the alignment there and then merging it with the current Silva database.

You mention that you have a contigs file, which suggests that you're looking at metagenomics data, so perhaps you want to try something like MG RAST http://metagenomics.anl.gov/ or PhylOTU http://www.ploscompbiol.org/article/...l.pcbi.1001061 which will get you phylogenetic information from a metagenomic rather than 16S dataset?


Silva http://www.arb-silva.de/ seems nice but i have more than 300 sequences
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Old 04-11-2011, 09:13 AM   #9
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Quote:
Originally Posted by Palecomic View Post
Sorry, just spotted your update. MEGAN would do the job, but check out that PhylOTU paper for a brief discussion of its limitations.
Megan asks me for a .RMA file... but i only have .txt and . fasta and .BlastClust and excel files... there is some conversion tool?
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Old 04-14-2011, 07:30 AM   #10
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Quote:
Originally Posted by Chuckytah View Post
Megan asks me for a .RMA file... but i only have .txt and . fasta and .BlastClust and excel files... there is some conversion tool?
Still don't know what to do

how can i have a .RMA file?
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Old 04-15-2011, 05:34 AM   #11
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This is from the manual:

Quote:
To prepare a dataset for use with MEGAN, one must first compare the given reads against a database of reference sequences, for example by performing a BLASTX search against the NCBI-NR database. The file of reads and the resulting BLAST file can then be directly imported into MEGAN and the program will automatically calculate a taxonomic classification of the reads and also, if desired, a functional classification, using either the SEED or KEGG classification, or both.
You import the blasta data to process it, but you can load processed megan results in .rma format.
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Old 04-15-2011, 08:09 AM   #12
Chuckytah
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Quote:
Originally Posted by themerlin View Post
This is from the manual:


You import the blasta data to process it, but you can load processed megan results in .rma format.
I will try it later ty so much
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Old 04-24-2011, 06:58 PM   #13
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Quote:
Originally Posted by themerlin View Post
This is from the manual:


You import the blasta data to process it, but you can load processed megan results in .rma format.
I don't have any blasta file... only fasta
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Old 04-25-2011, 03:03 AM   #14
JackieBadger
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Quote:
Originally Posted by Chuckytah View Post
Hello,

I have found this website: http://rdp.cme.msu.edu/classifier/classifier.jsp but it's for bacteria and archeobacteria...

don't know about one for all the kingdoms?

I have a contigs.fasta and i want to know how many sequences i have from wich taxonomic groups...
The Galaxy web portal has a MegaBlast tool, which will also build trees of your sequences highlighted by taxa. Watch the video tutorial on "Processing and analysis of 454 data in metagenomic studies"

http://main.g2.bx.psu.edu/
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Old 07-10-2011, 08:41 AM   #15
Chuckytah
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there are some tutorials for Megan???
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Old 10-29-2011, 12:37 PM   #16
Chuckytah
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Quote:
Originally Posted by JackieBadger View Post
The Galaxy web portal has a MegaBlast tool, which will also build trees of your sequences highlighted by taxa. Watch the video tutorial on "Processing and analysis of 454 data in metagenomic studies"

http://main.g2.bx.psu.edu/
Sorry, dunno why only saw your comment today. I will now watch the tutorial.
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Old 11-02-2011, 12:55 PM   #17
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Thanks for the comments everyone! I just downloaded MEGAN and got it working in just a couple minutes. I should always just check seqanswers first before trying to find something on my own...
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