Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bioperl blast parsing problem

    We recently upgraded our installation of blast from v2.2.19 to blast+ 2.2.26 and I have found that my bioperl blast xml parsers no longer work properly (typically they return some form of truncated result). Has anyone else encountered this and if this is a known problem have either the NCBI or BioPerl folks provided a solution.

    Thanks

    Mark

  • #2
    Which release of BioPerl are you using?

    Comment


    • #3
      version 1.006901

      Comment


      • #4
        Can't really help you there but have you considered other output formats (e.g. outfmt 6) and simply parsing your files with unix commands?
        savetherhino.org

        Comment


        • #5
          Unfortunately, you can't get the hit description via that method, a serious shortcoming.

          Comment


          • #6
            Originally posted by Mark View Post
            Unfortunately, you can't get the hit description via that method, a serious shortcoming.
            What do you mean by hit description? There are like 40 fields to choose from..
            Last edited by rhinoceros; 04-27-2013, 10:16 AM.
            savetherhino.org

            Comment


            • #7
              Subject description. Yes I know you could grab the oridinal ID and the go back to the blastdb and pull out the record and parse it's description from there but that's a bit of a pain so I would rather find out if there is a solution to the parsing of the xml output.

              Comment


              • #8
                You mean stitle/salltitles? But yeah, 2.2.28+ only.
                savetherhino.org

                Comment


                • #9
                  Yea, I know but I don't do the blast updates for our system and so can't take that route to a fix. Thanks for trying to help though.

                  Comment


                  • #10
                    Maybe your problem is related to an outdated XML::SAX? (first note). Just an idea..
                    savetherhino.org

                    Comment

                    Latest Articles

                    Collapse

                    • seqadmin
                      Current Approaches to Protein Sequencing
                      by seqadmin


                      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
                      04-04-2024, 04:25 PM
                    • 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

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, 04-11-2024, 12:08 PM
                    0 responses
                    11 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 04-10-2024, 10:19 PM
                    0 responses
                    17 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 04-10-2024, 09:21 AM
                    0 responses
                    14 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 04-04-2024, 09:00 AM
                    0 responses
                    43 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X