Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Create a feature table for 20,000 contigs

    Hi,
    We were generating 20,000+ set of contigs using Trinity for non-model organism (no genome).

    Next, we used blastx of these contigs versus swiss-prot to find homuloges.

    Now, we want to publish our contigs plus the blastx results as annotation dataset in genebank.

    Is that make sense to create an annotation dataset (for genebank) only from blastx?

    Thanks,
    Pap
    Last edited by papori; 09-28-2014, 01:46 AM.

  • #2
    Certainly people have published such annotations before. As for if the reviewers will be satisfied with that level of annotation depends on the journal and what level of detail you wish to provide.

    Comment


    • #3
      Originally posted by westerman View Post
      Certainly people have published such annotations before. As for if the reviewers will be satisfied with that level of annotation depends on the journal and what level of detail you wish to provide.
      Thanks westerman!
      Do you know a bout a tool/script which can covert the blastx results to a proper format for submission to genbank?

      Comment


      • #4
        Wondering out aloud, if it makes sense to submit this dataset to HTG (http://www.ncbi.nlm.nih.gov/genbank/htgs) or WGS (http://www.ncbi.nlm.nih.gov/genbank/wgs/? HTG may not available to individuals so WGS may be the only option.

        Was trying to think if one could get away without submitting annotations. Not the right application
        Last edited by GenoMax; 09-29-2014, 10:19 AM.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Wondering out aloud, if it makes sense to submit this dataset to HTG (http://www.ncbi.nlm.nih.gov/genbank/htgs) or WGS (http://www.ncbi.nlm.nih.gov/genbank/wgs/)? HTG may not available to individuals so WGS may be the only option.
          Thanks GenoMax!
          The data is transcriptome, not genome.
          So i am not sure this is relevant..

          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
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 10:19 PM
          0 responses
          17 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-10-2024, 09:21 AM
          0 responses
          14 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 04-04-2024, 09:00 AM
          0 responses
          43 views
          0 likes
          Last Post seqadmin  
          Working...
          X