need advice on PC software

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.
> Cheers
> --
> 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.

Jim Cassatt

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