Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • quickly extract amino acid sequence

    Hi all,

    I wonder if there is a handy tool or database to extract the amino acid sequence of a given coordinate on the human DNA. For example, given chr2:25457242, how to know what is the amino acid it is on and what are the flanking amino acids?

    Thank you!

  • #2
    I would assume a quick way would be if you couple bedtools getfasta with a tool such as VEP or snpeff...

    Comment


    • #3
      It will depend on the frame and orientation... You could make a short script extracting the nucleotides or the region (let's say 5 upstream and 5 downstream) and translate it yourself ...

      Comment


      • #4
        Originally posted by SylvainL View Post
        It will depend on the frame and orientation... You could make a short script extracting the nucleotides or the region (let's say 5 upstream and 5 downstream) and translate it yourself ...
        Thank you both. Yes it depends on the ORF and orientation. Technically, we have to concatenate the exon DNA sequences of a transcript and count the position of the mutation and translate the short sequences according to the ORF.

        Thanks!

        Comment


        • #5
          Get flanking DNA sequence for your locus, and do blastx against a database of proteins. Then parse the blastx results. Let blastx figure out the right frame and orientation.

          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, 03-27-2024, 06:37 PM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-27-2024, 06:07 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Working...
          X