Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Best method to get functional annotation ?

    Hi

    I have metagenomic contigs from an assembly. I'm looking for a pipeline to get functional annotation.
    I've used the soft FragGeneScan to get ORF that I mapped with Interproscan with Pfam and Tiger database.

    But it takes too long (I have 70 000 sequences out from FragGeneScan) so I'm asking if there is a better way to get automatic functional annotation ?

    I need GO numbers for my output .
    Thanks for your helps.

  • #2
    Perhaps blast2go is faster?

    Comment


    • #3
      I will try

      Comment


      • #4
        Unfortunately blast2go is not free.

        So Ive downloaded command line HMMER with database Uniprot, the output is a blast like with a list of hits and the domain name.

        eg:

        E-value score bias E-value score bias exp N Sequence Description
        ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
        + 6.6e-70 238.7 5.4 7.7e-70 238.5 5.4 1.0 1 sp|A1JMT1|MATP_YERE8 Macrodomain Ter protein OS=Yersinia en
        + 3.8e-69 236.3 4.1 4.2e-69 236.1 4.1 1.0 1 sp|Q7N603|MATP_PHOLL Macrodomain Ter protein OS=Photorhabdu

        But when I use HMMER on the website, I have access to accession number: do you know how can I get it with the command line HMMER ?

        Comment


        • #5
          Hi patouch74,

          I can't help you with your HMMER problem, but I'd like to add something to B2G.

          Though there is a "pro"-version of Blast2go, the main features (blast, go mapping, annotation, interpro scan integration) are also available in the free version. Just go to http://www.blast2go.com/start-blast2go and start the JAVA web-start with at least 4Gb RAM (the more, the better).
          With your dataset I would also suggest to separate your fasta file into 4-6 smaller ones and run them independently in Blast2GO (I have had some problems with the program when analyzing bigger datasets). The separated runs can be easily combined with a build-in command afterwards.

          btw: You mentioned that your previous method took you "too long". What exactly is to long for you? The Blast-step in Blast2GO could in your case easily take up to 1 week to finish...

          Comment


          • #6
            Hi WhatsOEver,
            Yes, I week is too long for me

            If someone know something else, I'll be glad to hear it.

            Comment


            • #7
              Originally posted by patouch74 View Post
              Hi WhatsOEver,
              Yes, I week is too long for me

              If someone know something else, I'll be glad to hear it.
              you could do a local blast in xml format and then upload the xml file to Blast2GO and start with the annotation process there.

              There is a web server to metagenome analysis MG-RAST http://metagenomics.anl.gov , but I don't know if that server retrieve GO terms.
              Last edited by juan.isaza; 05-29-2014, 12:06 PM.

              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
              25 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 10:19 PM
              0 responses
              28 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-10-2024, 09:21 AM
              0 responses
              24 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 04-04-2024, 09:00 AM
              0 responses
              52 views
              0 likes
              Last Post seqadmin  
              Working...
              X