Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • how to concatenate blast results (m8) via setting threshold of distance between hits

    hi, dear guys

    I performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance.

    however, these hits have no overlap, and what is interesting is that most gaps < 300bp (much shorter than full-length of the query sequence).

    so, how can i concatenate those closely related hits into one via setting a value (e.g 300bp) when these hits match the same subject (different regions), ——also to reduce the number of output hits per query.

    for example:



    are there any scripts or tools for this purpose?

    all your replies are welcome!
    Attached Files

  • #2
    It looks like you're blasting against a protein database and getting hits to CDS (i.e. the gaps represent introns or intergenic regions). If this is the case, you could just extract the ORFs and concatenate them by some simple command like cat. In any case, there must be a one-liner of cat grep cut and awk that would solve your problem..
    savetherhino.org

    Comment


    • #3
      Originally posted by rhinoceros View Post
      It looks like you're blasting against a protein database and getting hits to CDS (i.e. the gaps represent introns or intergenic regions). If this is the case, you could just extract the ORFs and concatenate them by some simple command like cat. In any case, there must be a one-liner of cat grep cut and awk that would solve your problem..
      thank you for your reply!
      actually, what you mentioned may typify one of the cases. then here i performed a tblastx using two genome sequences and found some of the hits per query had close relationship (certain significant colinearity) although each of the component hits seemed to be less related. so If I arbitrarily set a E/score value I think I will lose some informative hits.
      here I asked a general question for this kind of application, and I hope there is a versatile scripts...

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Latest Developments in Precision Medicine
        by seqadmin



        Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

        Somatic Genomics
        “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
        Yesterday, 01:16 PM
      • seqadmin
        Recent Advances in Sequencing Analysis Tools
        by seqadmin


        The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
        05-06-2024, 07:48 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 07:15 AM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 10:28 AM
      0 responses
      17 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-23-2024, 07:35 AM
      0 responses
      20 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 05-22-2024, 02:06 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Working...
      X