Hello,
I am a research associate in a new division of the core facility at Texas
Tech University with the responsibility to manage medium- to
high-throughput sequencing projects, mostly EST sequencing at this stage.
We have two Beckman's CEQ2000 sequencers, 2 Licor's dual-wave Readir 4200s
and Beckman's robot Biomek2000 used for miniprepping. I am at the point
when I need to set up data handling routine. We need to:
-edit (trim) raw sequence data
-put our sequences in GenBank-formatted files
-run BLAST searches against GenBank
-add top GenBank matches to sequence annotations
-submit finished sequence files to GenBank
-submit same files to our searchable databases on the local server
I anticipate to have 5 to 7 projects in the first year ranging in scale
from targeted 100 to 10,000 EST files per library. We are looking into
setting up separate local databases for individual species, current list
including HeLa cell line, mouse, wheat, sorghum, and cotton. Because of
this diversity and small scale of some projects, it is impractical, in my
opinion, to contract sequence handling out to a bioinformatics firm. I
would like to design an efficient semi-automated way of handling the steps
listed above by ourselves here. This would also give us a teaching and
demonstration opportunity which is important for us as a University.
Among the options already mentioned to me are the program called Factura
from ABI (only available in Mac version???) allowing to do sequence editing
(in batches?). We have Vector NTI package which is not intended for batch
analysis but could put data in GenBank-frmatted file. For batch BLAST
searches, I am currently exploring BLAST client software installation. I
guess batch submission to Genbank should be no problem. Presumably, I can
annotate sequences during Genbank submission. I don't know of any tool
available for automatic addition of top GenBank matches to sequence
annotations. This step will be probably most time intensive. We could
consider buying an existing program within our budget (1-2K), if available.
If nothing available, the question is what combination of procedures would
be most time and effort-efficient for our purposes.
I will appreciate any suggestion, in particuar, from anybody with similar
experiences/projects.
Thank you,
Natalya Klueva, Ph.D.
nklueva@ttacs.ttu.edu
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