I am looking into buying PC/Gene but I need to know a few things about it
first. I know that it is supposed to be able to search for
sequence similarity against a CDROM of Genebank or Swiss-Prot, but
it is also supposed to be able to search against personal databases.
My questions are this:
What file formats does it handle? I don't know what the format is
called, but there is an annotated format that is very common (I believe
it may be the Genbank format) That lists the Authors, the References,
Features, CDS, and DNA sequence. Does it handle this well?
What is the max size of the file? If I wanted to download the
genome sequence of H. Influenzae (a ~1.3 MEG file) could it search against
this? Or, if I downloaded the annoated version of this (the format
described in section one) which is ~3.5MEGS, could it handle this?
If not, what is the max size (in order to split such a large file up
into several files).
How fast is the search? I know this is an arbitrary question, but if you
are searching the entire genbank using one 1Kb DNA sequence, how long
would it take on your machine (I could extrapolate for faster Pentiums
or large hard-drives vs. CDROMS)?
Essentially, my main concern is whether to buy PC/Gene (and get the free
Win95 upgrade at the first of the year) or get GeneWorks for Mac (which
doesn't seem to do quite as much). On that note, if you have any experience
with Geneworks, I would apply the same questions above to that program,
since version 2.5 can also search personal databases. BTW, the demo
version of Geneworks doesn't give a good answer to these questions..
Thank you for any help
Chuck Miller
email: oravaxcm at world.std.com
