Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Blastn x megablast - homologous genes

    I have a list of nucleotide sequences (genes) and I would like to Blast against a list of nucleotide sequences from other species to check potential homologous sequences (orthologs and paralogs).

    Which blast is best for it? Blastn or Megablast?

    My smallest sequence has 12 nucleotides, and the largest has 16,000.

    Thanks
    Last edited by clarissaboschi; 02-01-2017, 01:31 PM.

  • #2
    This might be worth reading:

    Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
    or How To Use Sequence and Structure Information To Predict Protein
    Function. PLoS Comput Biol 4(10): e1000160.
    Protein structure prediction,Protein structure,Protein structure comparison,Protein structure databases,Sequence motif analysis,Structural genomics,Protein domains,Sequence alignment

    Comment


    • #3
      maubp it is a good paper, but did not help me, because is more focus in protein sequence analysis. I know is better to use protein sequences for it, but I need to use nucleotide sequences.

      I am wondering if in my case is better to use dc-megablast because I am searching sequences for cross-species comparisons.

      Comment


      • #4
        Sorry, you're right about the protein vs nucleotide focus.

        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
        49 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