Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • scaffold and contig

    Hi all,
    Does somebody know what's scaffold and the differences between scaffold and contigs? Thank you very much.

    Geng Chen

  • #2
    A contig is a contiguous length of genomic sequence.
    A scaffold is composed of contigs and gaps. Gap length can be guessed by incorporating information from paired ends or mate pairs (difference between the two).
    --
    Senthil Palanisami

    Comment


    • #3
      Thank you very much. I understand it now.

      Comment


      • #4
        Originally posted by m.shane
        This has been very helpful. I'd recommend the site to my Dad. he's into this kind of biz. Thank you so much for sharing this with us. More power to you and to your site!

        Scaffold <---this was a link to a store that sells construction scaffolding
        As a moderator, I should perhaps remove this post as it is off-topic and kind of spam. But, I won't, it is too funny...
        Last edited by ECO; 06-15-2011, 07:55 AM. Reason: removed spammers link

        Comment


        • #5
          at genbank's mallard genome ftp, they give an ~1.1GB fasta
          file of "unplaced scaffolds" with 78487 sequences
          of length 100-5998093
          When I try to match them to the chicken chromosome 1
          then I get a continuous distribution in matching subsequences.
          Shouldn't there be a sharp peak for those mallard "scaffolds"
          that are from chromosome 1 , shouldn't they be detectable this way ?

          15% of chicken and turkey 28-subsequences
          in chromosome 1 do match
          only ~3% in chicken vs.human or chr1 vs. chr2

          chromosomes are not available for mallards at genbank

          ftp://ftp.ncbi.nih.gov/genbank/genom...affolds/FASTA/

          ------------edit-------------------------------
          I found:
          > An in silico digest of the chicken genome, which is very similar [25,26], predicts similar genome
          > fractions of the RRLs of 4.1% for AluI, but only 0.2% for HhaI (data not shown).

          don't know what that means

          25. Fillon V, Vignoles M, Crooijmans RPMA, Groenen MAM, Zoorob R, Vignal A: FISH mapping
          of 57 BAC clones reveals strong conservation of synteny between Galliformes and
          Anseriformes. Anim Genet 2007, 38:303-307. PubMed Abstract | Publisher Full Text

          26. Skinner BM, Robertson LBW, Tempest HG, Langley EJ, Ioannou D, Fowler KE,
          Crooijmans RPMA, Hall AD, Griffin DK, Völker M: Comparative genomics in chicken and
          Pekin duck using FISH mapping and microarray analysis.
          BMC Genomics 2009, 10:357. PubMed Abstract | BioMed Central Full Text | PubMed Central
          ---------------------------------
          Last edited by gsgs; 06-28-2013, 10:13 PM.

          Comment


          • #6
            Originally posted by flxlex View Post
            As a moderator, I should perhaps remove this post as it is off-topic and kind of spam. But, I won't, it is too funny...
            Funny indeed
            I am looking forward to such a spam in the thread about deletion, inversion and insertion...

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Best Practices for Single-Cell Sequencing Analysis
              by seqadmin



              While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
              06-06-2024, 07:15 AM
            • seqadmin
              Latest Developments in Precision Medicine
              by seqadmin



              Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

              Somatic Genomics
              “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
              05-24-2024, 01:16 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, Today, 07:49 AM
            0 responses
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, Yesterday, 07:23 AM
            0 responses
            14 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-17-2024, 06:54 AM
            0 responses
            16 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 06-14-2024, 07:24 AM
            0 responses
            24 views
            0 likes
            Last Post seqadmin  
            Working...
            X