scaffold map for biarmipies annotation?

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cjones
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Location: Moravian College, Bethlehem PA
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scaffold map for biarmipies annotation?

Post by cjones » Tue Apr 23, 2013 12:14 am

I'm trying to identify the fosmid adjacent to 49 (a student has part of a gene near one end and based on the gene structure in Dmel there should be another three exons on the fosmid, but there's no trace of them via BLAST -- has the sequence degenrated or is the intron much larger in biarmipes?) -- where can I find maps of the biarmipes scaffolds?
Chris Jones
Assoc. Prof. of Biology
Moravian College
Bethlehem PA

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: scaffold map for biarmipies annotation?

Post by wleung » Tue Apr 23, 2013 1:49 am

The D. biarmipes projects are in order so contig48 and contig50 overlaps with contig49. I have created a new D. biarmipes project page on the GEP public wiki. The page contains a link to a text file with the exact location of each annotation project relative to the whole genome assembly.

You can search against the entire D. biarmipes assembly using FlyBase BLAST or by searching against the Whole-genome shotgun contigs (wgs) database and limiting the organism to Drosophila biarmipes (taxid:125945) at NCBI.

Note that the D. biarmipes assembly is currently a draft and both FlyBase and NCBI are periodically releasing updates to the whole genome assemblies.

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