In article <22015 at nuchat.UUCP> abbadon at nuchat.UUCP (David Neal) writes:
>>Are there any good programs for doing high speed sequence
>searches under unix?
>>I feel like there should be, but if there isn't, does any
>one have pointers to programming guides, databases,
>and/or government grant programs that might pay me
>to work on this and put the results in the public domain?
>>Since my specialty is CS/EE, please forgive my ignorance
>of the molecular biology field.
>
One of the more popular programs for rapid sequence searches
under unix is called the FASTA program package. A description of these
program was published in PNAS (1988) 85:2444 and more recently in
Methods in Enzymology, vol. 183 (1990) p. 63. This package of programs
can be used to search both DNA and protein sequence databases in a
variety of formats. It compiles under Unix SysV, BSD, Xenix, DOS, and
VMS. It is available via anonymous ftp from uvaarpa.Virginia.EDU in
the file /public_access/fasta14.shar. Copies are available for the
IBM/PC and Macintosh for a modest charge; send me electronic mail for
additional information.
Bill Pearson
