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  • 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


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


      • #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


        • #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

          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.


          • #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...


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