Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 1. embl/gbk to FASTA conversion; 2. 16s RNA to be found in a embl/gbk file

    I need help with 2 things:

    1. I have a EMBL or a gbk file format for the contigs of Salmonella enterica and I want to find the contig that has 16sRNA gene. Could anybody help me with this please?

    2. How can I convert EMBL/gbk to FASTA format?

  • #2
    If you have gff file and genome file, then you can extract fasta format sequences in many ways. here i know using Cufflinks source.
    gffread -E annotation.gff -o- | more
    Krishna

    Comment


    • #3
      Here is how this can be done with Biopieces:

      Code:
      read_genbank -i E_coli_K12_MG1655.gb |
      grab -k PRODUCT -p '16S ribosomal RNA' |
      rename_keys -k PRODUCT,SEQ_NAME |
      write_fasta -x
      read_embl can be used for embl files.

      Comment


      • #4
        Originally posted by ashuchawla View Post
        How can I convert EMBL/gbk to FASTA format?
        EMBOSS seqret will convert from EMBL to FASTA, GenBank to FASTA, etc:

        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
        51 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