PairWise and SearchWise new release

Ewan Birney birney at sanger.ac.uk
Mon Oct 7 05:27:28 EST 1996

**** 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


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(NB: for current users, notice that the OCMS Web site is no longer
maintained.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

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net