[BiO BB] anyone familiar with flybase or scaffolding nomenclature?

Fri Dec 28 08:22:20 EST 2007

Received the attached from a friend who was involved in the development of
flybase.  Hope it helps.  


Dennis J. Gurgul
Research Computing
Partners Health Care

-----Original Message-----
From: bio_bulletin-bounces at board [mailto:bio_bulletin-bounces at board] On Behalf
Of Mike Marchywka
Sent: Thursday, November 08, 2007 8:19 AM
To: bbb at bioinformatics.org
Subject: [BiO BB] anyone familiar with flybase or scaffolding nomenclature?

I read this


and thought it may be interesting to go get 12 assembled small genomes to
search for various polymoprhisms and test some code. I downloaded the
fasta files from flybase and hunted around their site for a while
but I couldn't figure out what the scaffold names mean or
if there is a set of assembled genomes somewhere. Anyone
have a link to relevant tutorial info? For that matter, can anyone suggest
another set of closely related organisms ( breeds within species
or cultivars among plants, I'm quite open to ideas) with small genomes
for testing?


Mike Marchywka
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