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  • 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...

  • #2
    Greengenes at Lawrence Livermore will help you with that, in concert with ARB.

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    • #3
      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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      • #4
        I think he means this website;

        http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

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        • #5
          Originally posted by boetsie View Post
          thank you. Someone advised me to use MEGAN... what you think?

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          • #6
            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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            • #7
              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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              • #8
                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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                • #9
                  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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                  • #10
                    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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                    • #11
                      This is from the manual:

                      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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                      • #12
                        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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                        • #13
                          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

                          Comment


                          • #14
                            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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                            • #15
                              there are some tutorials for Megan???

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