Tweet
Hi all,
Does somebody know what's scaffold and the differences between scaffold and contigs? Thank you very much.
Geng Chen
Does somebody know what's scaffold and the differences between scaffold and contigs? Thank you very much.
Geng Chen
-
-
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 -
Thank you very much. I understand it now.
Comment
-
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...Originally posted by m.shaneComment
-
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
-
Funny indeedOriginally posted by flxlex View Post
I am looking forward to such a spam in the thread about deletion, inversion and insertion...Comment
-
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...Today, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM
Comment