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  • gene annotation for a large number of genes

    Hello,

    I have around 60 000 genes from RNA-seq data. I have blasted each sequence to the nr database and obtained a xml file. Does anybody know what softwares can be used for down stream GO term mapping and annotation by using the xml file as input? Thanks.
    Last edited by Tom2013; 10-13-2015, 07:14 AM.

  • #2
    Which species ? Pedant is good


    Some use Blast2go but I always had network problems with it several years ago.

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    • #3
      Blast2GO will accept your NCBI Blast+ generated XML file for import. You can provide one file of multiple XMLs, multiple files as well as a folder. Blast2GO supports the latest version XML2 as well as the previous XML format. Mapping the HIT ids against the GO and further functional annotation should be straightforward.

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      • #4
        Thanks for your replies. I have done annotation.

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        • #5
          Did you use one of the options mentioned above or something different? It would be useful to include that information for benefit of others who find this thread via a search in future.

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          • #6
            I used blast2go for mapping and annotation. The B2G pro is very fast for GO term mapping and it is very easy to use.

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