Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Removing similar sequence reads

    Dear All

    I am looking for a fast way to remove similar sequence reads or to find unique records.

    I have 7 large fasta files with about 2 *10^6 short sequence reads in each. I have collapsed each file (removed identical sequences) in order to decrease file size. Now I would like to compare two files at a time and find all the unique sequences for each file. It is easy to remove identical records but in my case I would also like to find (highly) similar sequences. I tried blastn -task blastn-short (because the sequences are <100nt) but it takes a long time even with -num_threads 10. Megablast would be faster but I think it will not work with short sequences. Any suggestions?

    Thank you very much and I am looking forward to your replies

  • #2
    Have a look at Uclust

    Comment


    • #3
      Maybe PatternHunter?

      Comment


      • #4
        Are the sequences you are wanting to compare between files of the same length? (if that's the case, edit distance calculation would be a handy trick).
        Last edited by cedance; 10-14-2011, 07:44 AM.

        Comment


        • #5
          Dear maasha,

          I tried usearch/sort/cluster and it works fine. Thanks a lot!

          Dear biznatch,

          I checked out the PatternHunter website. I guess I could use the homology search tool but I did not bother with getting a trial version since I was not sure how much a license will be at the end. Thanks for the suggestion though.

          Dear cedance,

          no the sequences are of different length. Good idea but I guess it work only for aligned sequences. Thanks!

          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
          51 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