Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Best hit alignment in offline Blast

    Hello. Can anyone let me know the proper command and syntax for best hit alignment in offline blast? The blast manual lists is not very clear on this topic, and I cannot seem to find much information about this elsewhere on the net. Should i use only -best_hit_overhang & -best_hit_score_edge as the two options for getting a best hit alignment? Also, what would be an optimal parameters for -best_hit_score_edge? My dataset contains lots of smaller sequences (roughly about 100 bases in length), so I would want them to be ideally covered in my blast sequences. Thanks a ton!

  • #2
    Usually BLAST reports the found HSP ordered. Which means that the first hit reported also is the best hit with respect to E-value / Bit Score... so you just want to parse the first hit from every input-sequence. You have to keep in mind that if there are hits that are equally good you end up with kind of ambigous results because they are still listed.

    Comment


    • #3
      Originally posted by sphil View Post
      You have to keep in mind that if there are hits that are equally good you end up with kind of ambigous results because they are still listed.
      This is what I am afraid of if I blast my sequences to the NR or NT database. To circumvent this, since I am dealing with human data, I am blasting only against Human est sequences. I am hoping this will take care of the problem.

      Thanks a lot for your wise words Phil! appreciate you taking time out to reply
      Last edited by ron128; 11-13-2013, 10:44 AM. Reason: forgot to thank user!

      Comment


      • #4
        no worries...!

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          02-10-2025, 01:58 PM
        • seqadmin
          An Introduction to the Technologies Transforming Precision Medicine
          by seqadmin


          In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
          01-27-2025, 07:46 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 02-07-2025, 09:30 AM
        0 responses
        72 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-05-2025, 10:34 AM
        0 responses
        113 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-03-2025, 09:07 AM
        0 responses
        90 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 01-31-2025, 08:31 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Working...
        X