Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Alignment of multiple sequences to one (fixed) reference

    Hi all,
    I have a reference sequence, which is shorter than the sequences I want to align. The first sequence is my reference, so it should be more or less fixed. The other sequences are locally or in some cases globally similar. Because my reference sequence is shorter than the other sequences, I'm not able to map the other sequences on that. If I do multiple sequence alignment, there are gaps inserted in the reference, which shouldn't be there. If I do pairwise alignments I miss the graphical representation of all sequences to my reference, I can only investigate each sequence pair individually.
    Is there an alignment toll, which provides multiple pairwise sequence alignments with a good visualization of the results? Or a multiple sequence alignments with one anchor sequence? I only found the seed option in mafft, but this only works for a seed alignment not a seed sequence. Am I right?
    Thank you for every answer!

  • #2
    How long are your sequences?

    If they are relatively short, you could use bowtie1, which doesn't do gapped alignment, but I think the longest sequence it will map to the reference is about 1000 bp.

    Comment


    • #3
      My reference is ~4500 bp long. The other sequences are from 400bp - 9000bp I'm also interested in the overlapping region next to the reference. The reference should not contain gaps, while the other sequences might contain gaps. Maybe it's problematic if they contain indels.

      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
      11 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      10 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
      68 views
      0 likes
      Last Post seqadmin  
      Working...
      X