HI.. help on sequence analysis

Harry Mangalam mangalam at uci.edu
Wed Mar 3 13:35:11 EST 1999


If you can define them in IUPAC codes, tacg can find them (with
specified # of errors, in degenerate sequence of any length).  If you
want to run the commandline app, you can download it at:
ftp://mamba.bio.uci.edu/pub/tacg

If you want to use the somewhat less capable, but easier-to-use Web
interface, you can go to:
http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.form.html

But you'll have to upload your own GCG-REBASE formatted file containing
the sequences you want to find.  There's an example of what you have to
do there.

Alternatively, there are many such programs that can do this, depending
on your sequence length (is is a KB or multiple Megabases?), complexity
of patterns (do you need to be able to search for a regular expression?
and IUPAC expression? a profile? with errors? both strands
simultaneously?), number of patters to search for at once time, whether
you need to be able to handle degenerate sequence input, etc.  

- the 'grep/egrep/agrep' family of regular expression matchers may be
good enough for you.
- grepseq is a very fast biosequence version of agrep, but has some
interface peculiarities.
- GCG's findpatterns is quite robust but it's ... GCG, and $ware.
- DNAStrider and most commercial apps have such capabilities built in,
but (strangely) many don't allow searching with errors or even with
IUPAC codes or even regular expressions.



jayakumar wrote:
>     Does anyone know of any softwares which can check a sequence for the
> presence of terminators, promoters, SD sequences etc.
-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2899 -- mangalam at home.com




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