Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • NCBI feature table (.tbl) format

    I'm writing a script to generate a .tbl file from our genome annotation pipeline for processing by tbl2asn and submission to GenBank. I have a bunch of partial features, which are supposed to be indicated with arrow (< >) symbols. I think I have the forward strands figured out. What I don't know about is the referse strand.

    Here's an example of a reverse strand gene where the end of the gene is unknown.:

    Code:
    Feature Scaffold_1044.1
    <250    32      gene
                            locus_tag       CFIO01_11959
    <250    198     CDS
    149     32
                            locus_tag       CFIO01_11959
                            product  Hypothetical Protein
                            protein_id      gnl|ThonCIALE|CFIO01_11959
                            transcript_id   gnl|ThonCIALE|mrna.CFIO01_11959
                            codon_start     1
    <250    198     mRNA
    149     32
                            locus_tag       CFIO01_11959
                            product  Hypothetical Protein
                            protein_id      gnl|ThonCIALE|CFIO01_11959
                            transcript_id   gnl|ThonCIALE|mrna.CFIO01_11959
    Problem is, tbl2asn still complains that the gene is missing a stop codon, so I guess it didn't recognize my arrow symbol. Does anyone have an example tbl file with partial features?

  • #2
    Here are some example .tbl files: http://www.ncbi.nlm.nih.gov/genbank/examples.wgs

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM
    • 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

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    30 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    32 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    28 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Working...
    X