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  • Which BLAST output format can give full taxonomony information

    Hi, I was wondering which BLAST output format I should use to do this. I want to blast against nt database. I want the output not only gives me genus and species name, but also gives me phylum, order, family name.

    Is it possible?

  • #2
    you can use the GI number to map the tax id and the get the complete taxonomic lineage information via taxdump.tar.Z. ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

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    • #3
      Is it possible to map it when I blast it? or I need to get blast result first and then map to tax?

      Which command I should use to map the tax id?

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      • #4
        blast output format 6, 7, and 10 can be additionally configured to produce a custom format , it includes the Subject Taxonomy ID (staxids flag),
        for example:
        blastx -query Human_kinase_rna-100.fasta -db ../ccds/CCDS_protein.20130430 -out Human_kinase-rna-blastx-m7.tbl -evalue 1 -outfmt “7 qseqid qlen slen qcovhsp sseqid staxids bitscore score evalue pident qstart qend sstart send” -num_alignments 10 -num_threads 8
        I use a perl script to fetch the complete taxonomic lineage information of the blast staxids.

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        • #5
          Originally posted by jameslz View Post
          blast output format 6, 7, and 10 can be additionally configured to produce a custom format , it includes the Subject Taxonomy ID (staxids flag),
          for example:

          I use a perl script to fetch the complete taxonomic lineage information of the blast staxids.
          Do I need to put the complete taxonomic lineage information file (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/) in the same folder with my database file? In your example, I didn't see your command call any taxonomic lineage information file.

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          • #6
            Hi use format 7 and use your command settings

            I still do have the taxonomic lineage and I don't know how to use the taxonomic lineage file

            Here is my output.

            query id query length subject length % hsp coverage subject id subject tax ids bit score score evalue % identity q. start q. end s. start " s. end "
            denovo0 266 297 85 gi|14718977|gb|AF352544.1| 163259 351 190 1.00E-93 95.15 39 265 1 219
            denovo1 400 1178 100 gi|117572484|gb|DQ979290.1| 1211 706 382 0 98.5 1 400 670 1069

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            • #7
              Usage:
              perl tax_trace.pl nodes.dmp names.dmp taxids.txt taxids_export.txt
              input file:taxids.txt
              format: seqId taxId
              gl00001 192
              gl00002 2020
              nodes.dmp names.dmp can be download from taxdump.tar.Z (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)


              output file:taxids_export.txt
              gl00001 Azospirillum brasilense root|cellular organisms|Bacteria|Proteobacteria|Alphaproteobacteria|Rhodospirillales|Rhodospirillaceae|Azospirillum|Azospirillum brasilense no rank|no rank|superkingdom|phylum|class|order|family|genus|species
              gl00002 Thermomonospora curvata root|cellular organisms|Bacteria|Actinobacteria|Actinobacteria|Actinobacteridae|Actinomycetales|Streptosporangineae|Thermomonosporaceae|Thermomonospora|Thermomonospora curvata no rank|no rank|superkingdom|phylum|class|subclass|order|suborder|family|genus|species
              Attached Files

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              • #8
                Originally posted by jameslz View Post
                Usage:


                input file:taxids.txt
                format: seqId taxId


                nodes.dmp names.dmp can be download from taxdump.tar.Z (ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)


                output file:taxids_export.txt
                Thank you. Can you also post your "taxids.txt" and "taxids_export.txt" file. I need to make sure my input file format is right and the output file is what I want. The attachment is my blastoutput and taxid. It didn't work.
                Thank you.
                Attached Files
                Last edited by SDPA_Pet; 02-19-2014, 08:32 AM.

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                • #9
                  You can parse the blast out file using:
                  cut -f1,6 blastout.txt >taxids.txt
                  and then:
                  perl tax_trace.pl nodes.dmp names.dmp taxids.txt taxids_export.txt

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                  • #10
                    Hi, what does this mean? "cut -f1,6 blastout.txt >taxids.txt"

                    Comment


                    • #11
                      Originally posted by SDPA_Pet View Post
                      Hi, what does this mean? "cut -f1,6 blastout.txt >taxids.txt"
                      Linux Command, Get the first and the sixth collumn (taxids)

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                      • #12
                        Oh, my taxon id is the 5th column. I have another attachment in my post. Is that correct? I can't get taxon information from that file.

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                        • #13
                          Just fetch the "query id" and "tax ids" collumn .

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                          • #14
                            Which BLAST output format can give full taxonomony information?

                            Not the XML output (for now), but the optional taxonomy columns in the tabular/comma separated output get you close:
                            For some time I had thought that the best option for computer parsing of BLAST+ output was BLAST XML. It had all the key bits of information...

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                            • #15
                              I think blast+ has option to include taxonomy information. the "sscinames" option --- unique Subject Scientific Name(s)

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