Hi folks,
I am setting up a large ABI facility for genome sequencing. We have a very
good existing set-up for radioactive sequencing using DNAstar programs and some
handy home-made database management software. However, we are a trifle lacking
in the ABI support. Plans are for several more machines, so I need to evaluate
software now.
One of our biggest problems concerning the ABI output are variable regions of
non-homologous "junk" at the 3' and 5' ends of the sequence files. Our current
assmebly programs do not like this fuzzy region and it has proven difficult to
construct contigs from these files.
I was wondering if anyone has tried the ABI Macintosh program packages: INHERIT
and SEQUENCE NAVIGATOR. Has ABI addressed what this common problem of "junk"
sequence in these programs? How about database management of sequencing
projects?
\ \ / \ \ / \ \ / \ \ / George Mayhew \ / \ \ / \ \ / \ \ /
\__\/ \__\/ \__\/ \mayhew at genetics.wisc.edu\/ \__\/ \__\/ \__\
George,
We have had to deal with the same problem in our core lab. I have found the
ABI software totally inadequate for sequence assembly and far too time
consuming for even routine file management of sequences. We have been using
"Sequencher" from Gene Codes Co. (Ann Arbor, MI) which works fairly well.
The nicest feature of this program is automatic vector removal. For short
inserts where you get vector at the 3' end, you can totally ignore the bad
sequence at the end of the run. For large inserts we usually truncate the
seq. either automatically at 500 bp, or wherever the "NNN's" start to appear.
After using the assemble functions and putting together the contigs, we can
then restore the crummy 3' end sequence to help editing ambiguities. There is
just no point trying to use bad sequence to assemble contigs.
Stuart Brown | Plant Genetic Resources
| Georgia Experiment Station
INTERNET: | 1109 Experiment Street
SBROWN at GAES.GRIFFIN.PEACHNET.EDU | Griffin, Georgia 30223-1797 USA
BITNET: SBROWN at GRIFFIN | Fax: 404-229-3323
