Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment


    • #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.

      Comment


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

        Comment


        • #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.

          Comment


          • #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.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-27-2024, 06:37 PM
            0 responses
            13 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-27-2024, 06:07 PM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            53 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            69 views
            0 likes
            Last Post seqadmin  
            Working...
            X