ANNOUNCE: IBM-PC Sequence Analysis Freeware

Gord Hutchinson hutch at NetShop.bc.ca
Thu Jul 11 23:11:53 EST 1996


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This posting announces new versions of 3 separate programs that run on
IBM-PC clones. The three programs are fully functional (i.e. not demos)
and are freeware. They are:

SorFind, Version 2.8 (download as sorfin28.exe)

	SorFind predicts coding exons in vertebrate genomic DNA. An
independent analysis has recently shown the program to have an accuracy
similar to GRAIL II. (Burset and Guigo, Genomics, in press). 

RepFind, Version 1.7 (download as repfin17.exe)

	RepFind identifies common repetitive elements in DNA sequence.
The default files are set up to identify primate repeats, such as Alus,
L1s, MERs, LTRs etc.  The program is user-extendible to identify any 
repetitive sequence of interest in any organism. The program can also be
used to identify and annotate vector contamination. As an option, repeats
or vector sequence can be masked with the letter "n" to facilitate 
database searches. 

PromFind, Version 1.1 (download as profin11.exe)

	PromFind  predicts promoter regions in vertebrate DNA sequence. It 
currently is able to identify 60 to 70 percent of promoter regions of 300 
bp width to within 200 bp. No prior knowledge of transcription element 
binding sites is assumed. This program will be published shortly (revised 
manuscript submitted to CABIOS). 

All three programs accept sequence in plain, Fasta, EMBL or GenBank format,
and output the sequence, with an added feature table, in EMBL or GenBank
format. The programs can be "piped" into one another, allowing the 
simultaneous identification of promoters, coding exons and repetitive 
sequence using one command line. A manual is included for each program.

The binary executable IBM-PC programs are free of charge. There is also
a full GUI under development, but that will be commercial. There are
no conditions attached to the use of the DOS programs except that there 
is no associated warranty.

The three programs have been uploaded to the following servers as of
July 9, 1996:

ftp://iubio.bio.indiana.edu/molbio/ibmpc (there now)

ftp://ftp.bchs.uh.edu (currently inaccessible in /gene-server/incoming
	but hopefully will be moved to /gene-server/dos

ftp://cgat.bch.umontreal.ca (currently in the /incoming directory)

Comments, bug reports and suggestions for new features are welcome and
should be sent by email to hutch at netshop.bc.ca. Inquiries can be addressed
to:

Dr. Gordon B. Hutchinson
Department of Medical Genetics
University of British Columbia
Canada

Mailing Address:
c/o RabbitHutch Biotechnology Corporation
P.O. Box 506
108 Mile Ranch, B.C.
V0K 2Z0 Canada

Phone:	(604)791-1937
Fax:	(604)791-1938
E-mail: hutch at netshop.bc.ca






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