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

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(NB: for current users, notice that the OCMS Web site is no longer
maintained.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




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