need advice on PC software
CZJ at CU.NIH.GOV
CZJ at CU.NIH.GOV
Fri Dec 11 09:06:32 EST 1992
> I would like to solicit the advice of readers of this group
> regarding software available for the PC to assist with molecular
> biology. Shareware or public domain would be best, as our budget
> is limited, but I am also interested in comercial packages.
> What we are interested in is software which will assemble sequences
> (from multiple overlapping sequence files), identify restriction sites,
> open reading frames, do translations and alignments.
> If you know of one or more software packages which do these things, please
> e-mail me and let me know. I am also particularly interested in your
> opinions on the functionality of these packages, so if you would care
> to pass on any experience you have had I would appriecate it.
> bcrawfor at Sol.UVic.CA -- member of the society for simple .signatures (SSS)
The package I like is Seqaid from Don Roufa's laboratory.
It does many of the things that the commercial packages do and
has a usable interface. The one thing it does not do is take a
sequence and compare it with the rest of the sequence database
(protein or nucleic acid). That can be done, however, using the
various e-mail blast servers that are available.
Another package I like is Kay Hofmann's Prograph. This package
allows the analysis of protein sequences.
Both of these packages are available on the embl mail server and
the usual ftp sites.
I also hear from the grapevine that the Protein Data Bank (the
Brookhaven Crystallographic database) will in the next few months
be putting out its database on CD-ROM (already happening) with
software to view the structure on a PC.
The combinations of all of these packages, together with the NCBI
Entrez software, lets one do a lot for a little--especially given
the price of PC clones these days.
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