Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Performing many pairwise alignments

    Hi all,

    I've stumbled into an issue in my analysis for which I haven't been able to think of a single solution.
    I have ~4,000 distinct pairs of orthologous sequences, and I would like to have global alignments for each pair. I am not interested in a multiple sequence alignment, but simply distinct pairwise alignments. In papers with similar-sized data sets, authors have briefly mentioned that they used standard alignment programs, like ClustalW, MUSCLE, or T-Coffee. However, short of inputing each pair of sequences at a time into these programs (i.e. thousands of inputs!), I haven't been able to understand how that can be done in those programs. As far as I can tell, the set of sequences one supplies as input will undergo a multiple sequence alignment.

    Am I missing something in how to use those programs for this problem? Or is this an issue that must be dealt with Perl programming?

    Any insights would be greatly appreciated!

    Thanks!

  • #2
    This sounds like a situation where you really need a script. You don't say how your data is currently structured, but you'll probably only need a very simple script to automate the submission of 4000 jobs to any alignment program.

    Of course your next problem will be what to do with 4000 pairwise alignments, so you'll probably need a script for that too eventually...

    Comment


    • #3
      Try needleall from EMBOSS 6.2.0 or later for many-to-many Needleman-Wunsch global alignment:

      Comment


      • #4
        Thanks! That helps a lot! I tried EMBOSS's needleall, and it does wonderfully in aligning pairs, but I still need to do some scripting to parse that output. Eventually, I want to have each alignment in Phylip format for PAML.

        Cheers!

        Comment


        • #5
          The EMBOSS tools support a range of output files, but you may still need some scripting...

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Exploring the Dynamics of the Tumor Microenvironment
            by seqadmin




            The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
            07-08-2024, 03:19 PM
          • seqadmin
            Exploring Human Diversity Through Large-Scale Omics
            by seqadmin


            In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
            06-25-2024, 06:43 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 07:20 AM
          0 responses
          23 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-16-2024, 05:49 AM
          0 responses
          38 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-15-2024, 06:53 AM
          0 responses
          44 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 07-10-2024, 07:30 AM
          0 responses
          41 views
          0 likes
          Last Post seqadmin  
          Working...
          X