Hello,
Recently, I have been reviewing options in a few of the areas
listed
in the below emails.
Sequence analysis, data management, ect.
Some time ago there had been a reference for comparison of DNA
Sequence analysis software features. I found the sheet of paper I
had printed out, however, it has no reference. It lists various
sequence
analysis software packages followed by simply having an X in a column if
the package has a particular feature. Some of the features include, but
not limited to, editing, fragment assembly, sequence comparison,
database
searching, data management, ect. Some of the information has changed,
but
it could give you somewhere to start. I will scan the information and
send it only to those who request the information. I do not wish to
offend
others on the list with excess information.
Jennifer Brosius
Sequencing Technologist
ValiGen
300 Pheasant Run
Newtown, PA 18940
Phone:(215) 504-4444
Fax:(215)504-1546
jbrosius@kimeragen.com
http://www.Valigen.net
Does anyone have experience with a laboratory information management
system (LIMS) for a genotyping and sequencing lab? We are considering
ABI's products, SQL*GT for data tracking and BioLIMS for data
management. Any input, good or bad, would be appreciated!
Thanks,
Tim Howard, Ph.D.
Center for the Genetics of Asthma & Complex Diseases
University of Maryland, Baltimore
108 N. Greene St.
Baltimore, MD 21201
Ph: (410) 706-1690
FAX: (410) 706-1644
-----Original Message-----
From: San Francisco [mailto:pxida@TTACS.TTU.EDU]
Sent: Wednesday, May 03, 2000 4:54 PM
To: Recipients of ABRF List
Subject: data handling
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.eduHi all,
This archive was generated by hypermail 2b29 : Thu May 18 2000 - 09:47:34 EDT