In article <39rq3m$d9r at news.doit.wisc.edu>,
mayhew at midgaard.genetics.wisc.edu (George Mayhew) wrote:
> 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?
>> Any insights, opinions, experiences, etc. would be extrememly helpful
> Especially any good experiences, since I'll have to take this up with the
> "big-boss" and it would be helpful to have ammunition first! ;-)
as a sequence analysis program, Navigator isn't very good IMHO, however,
for what you seem to want it for it is perfect. you can set up a number of
ambiguity cut-off parameters for your sequence and just plug the files from
the Analysis program into it and let it do it's job. you can also use it
to call ambiguous bases automatically and batch up similar or identical
sequences. i don't know of another program that does this, so if you're
going to switch to ABI autosequencing, it would definitely be worth your
while to get this program and a computer to dedicate to it.
good luck,
eric
--
*************************************
*Of course it's not true... *
*But let's make the bastard deny it!*
* LBJ (1948) *
*************************************
eric c. anderson
anderson at pharmdec.wustl.edu
dept. of molecular bio. and pharm. (314)362-3963 (lab)
washington univ. school of medicine (314)862-2435 (home)
660 s. euclid box 8103 (314)362-7058 (FAX)
st. louis, mo 63110
