**** PairWise and SearchWise 1.6.2 ****
*** Beta-Release ***
PairWise and SearchWise version 1.6 has been released for
general use. Some of the improvements include:
o On-the-fly parsing of EMBL format databases to provide only
genomic or only cDNA sequences during database searching
o Configurable SRS linking in the HTML output
o HTML output of the alignments
A considerable number of bugs have also been removed.
For people who have not used PairWise and SearchWise, they are
programs which can trace a match of a protein sequence or a protein
profile to a DNA sequence allowing for frameshifts and intron in the
DNA sequence. This work has been recently published in the July issue
of NAR
"PairWise and SearchWise: finding the optimal alignment
in a simultaneous comparison of a protein profile against all DNA
translation frames" Ewan Birney, Julie Thompson and Toby Gibson
Nucleic Acids Res., 24 2730-2739, 1996
There is a web site at
http://www.sanger.ac.uk/~birney/wise/topwise.html
and the source code, and hopefully a collection of binaries are
available at
ftp.sanger.ac.uk /pub/birney/wise
The WWW site has an extensive series of help/tutorial and installation
files to guide you towards making use of PairWise and SearchWise. I
would read some of the files first before downloading.
(NB: for current users, notice that the OCMS Web site is no longer
maintained. The Sanger centre site will be the main site for at least
the next 3 years - please update any links you have).
There is a mailing list for people who would like to be in
closer contact with releases, and for any other information, please
email me at
birney at sanger.ac.uk
Have fun!
ewan birney
