Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Rfam/infernal help running

    Hi all,

    I am trying to use rfam to search for sequence homologs to many small RNAs (read lists of about 50,000 sequences).

    I have successfully installed infernal and downloaded the rfam database. I am unclear on if/how I need to prepare the rfam database using cmbuild, cmcalibrate, and cmsearch. (I saw this in a tutorial for searching a sequence database with a single covariance model). When I tried this, cmbuild worked but cmcalibrate gave an error. Or, is rfam already in the correct format? If so, what are the steps to run a search? Or can you point me to the appropriate tutorial?

    Any help on how to run rfam using infernal would be greatly appreciated!

    Thanks very much,
    Claire

  • #2
    What exactly is the error?

    Running it is easy, if you use the perl script provided at the website (rfam_scan.pl).

    Command:
    perl rfam_scan.pl -blastdb /home/Data/RFAM/Rfam.fasta -o /home/Data/RFAM_output.txt --bt 0.0001 --nobig /home/Data/RFAM/Rfam.cm /home/Data/input.fasta

    (evalue: empirical from my site; --nobig: Doesn't scan for the big rRNA subunits; rnammer is way faster for that)

    Comment


    • #3
      Hi Claire,

      if you have downloaded the Rfam.cm from the Rfam website (ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/), then you only have to run cmpress on the Rfam.cm file to prepare it for cmscan (infernal v1.1).

      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, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X