Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • SCOPE++: A tool for homopolymer identification

    We are in the process of releasing a software tool SCOPE++ (Sequence Classification Of homoPolymer Emissions).

    It has the capability to identify homopolymer sequences using Hidden Markov Models, allowing for fast, accurate and robust identification.

    Additionally, poly(A)/poly(T) trimming is supported.

    The executable can be found at the following website:

    HTML Code:
    http://code.google.com/p/scopeplusplus/

  • #2
    Could you explain why you choose to use HMM to detect homopolymer stretches? Why not use some simple perl code such as

    Code:
    $seq=uc($seq);
    while ($seq=~/(A+|C+|G+|T+)/g){
    	$homopolymer_length = length($1);
    	...
    }
    Or is your code meant to detect imperfect long homoloymers?

    Comment


    • #3
      hmm double posting here
      Dealing with customer samples, data, and the challenges that come with both?

      to TS I think it's more helpful to have all comments on a single thread yeah?
      http://kevin-gattaca.blogspot.com/

      Comment


      • #4
        @flxlex:

        Yup. It is used for detecting imperfect homopolymers. This is particularly useful when identifying poly(A) tails. Since base miscalls tend to become more frequent towards the ends of sequence reads, you aren't expected to identify perfect poly(A) tails.

        @KevinLam:

        Yeah. My bad. I'm linking these two threads.
        Last edited by noms; 04-13-2012, 12:06 AM.

        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