Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Contig order on Genbank

    A bacterial species I am interested in has had it genome sequenced but is only available as contigs on Genbank. These contigs are numbered. Can anybody tell me if these contigs are in order?

    I want to upload them to RAST and am wondering can they just be uploaded as is from genbank.

    Thanks

  • #2
    Unless something has changed the contigs are not likely to be "ordered" meaningfully (other than perhaps largest to smallest or vice-varsa) for an "unfinished" genome. You may need to dig through the supplementary material associated with the submission to see if there is any information.

    Comment


    • #3
      Thanks genomax.

      If I use a tool such as emboss union will this order the contigs for me? I tried mauve but I keep getting an error. I can input the contigs to emboss union which gives me 1 full sequence for all removing the overlapping regions.

      I am pretty new to all this and my basis is that if it joins them in a way that removes the overlapping regions then they are in the correct order. But I could be way off base!

      Comment


      • #4
        If the contigs are truly overlapping this easily then the folks who originally submitted the sequence would have discovered that (unless this was an automated whole genome survey type sequence submission). But since they did not perhaps there was a reason.

        Is there a closely related genome available (that is "finished"/annotated) in GenBank? If there is then you could compare the contig resulting from Emboss union to the finished genome. Just because an informatics tool produced an output does not mean that the result is right. This is where domain knowledge expertise needs to come in to decide if the result looks reasonable/acceptable.
        Last edited by GenoMax; 12-09-2013, 06:30 AM.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          The Impact of AI in Genomic Medicine
          by seqadmin



          Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
          02-26-2024, 02:07 PM
        • seqadmin
          Multiomics Techniques Advancing Disease Research
          by seqadmin


          New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

          A major leap in the field has
          ...
          02-08-2024, 06:33 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:12 AM
        0 responses
        19 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-23-2024, 04:11 PM
        0 responses
        67 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2024, 08:52 AM
        0 responses
        74 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-20-2024, 08:57 AM
        0 responses
        65 views
        0 likes
        Last Post seqadmin  
        Working...
        X