PC/Gene, OMIGA

Rodrigo Lopez rls at ebi.ac.uk
Mon Mar 23 06:50:26 EST 1998


"Berke, Tamas" wrote in message
<205969B4B7A2D11181F600805FBB80EA05164A at chkd.evms.edu>...
>Dear All:
>
>I recently learned that PC/Gene (latest version 6.85) is no longer
supported
>by the developer.
>I was recommended OMIGA to replace it which is a new Win95-based program
for
>sequence database and basic manipulation.
>Still evaluating it, I am not convinced yet that OMIGA can really replace
>PC/Gene.
>I might need to spend more time with OMIGA, however, in the meantime, I'd
>like to get some idea from you for a Win95 program for maintaining nt and
aa
>sequence databases and performing basic analysis on those (incl. pairwise
>and multiple alignment, translation, database homology search).
>Thanks for your input.
>
>Tamas Berke
>Norfolk, VA

This is an unofficial reply but I hope it helps.

Maintenance of nt and aa databases under windows: Why not try EMBL Search.
This program is a free database and query retrieval system for the MAC as
well as PCs running windows (3.1x, 95 and NT). Please check
ftp.ebi.ac.uk/pub/software/mac
and ftp.ebi.ac.uk/pub/software/dos. Alternatively contact kasia at ebi.ac.uk
who will be quite happy to provide more information.


1. Database homologies searches:fasta and blastall which can be found at
   various sites:
        check: ftp.ebi.ac.uk, ncbi.nlm.nih.gov, ftp.virginia.edu and
               ftp.bio.indiana.edu
2. Multiple alignments:
       check clustalw and clustalx: ftp.ebi.ac.uk/pub/software/dos/clustalw
and
       ftp.ebi.ac.uk/pub/software/dos/clustalw/clustalx

3. Paiwise alignments:
       check Macaw from ncbi.nlm.nih.gov (also at the EBI ftp.ebi.ac.uk)

There are various site which permit you to do some of the thing you want on
the WWW.
The list is long but a little excursion will set you in the right track:

www.ebi.ac.uk, www2.ebi.ac.uk
www.expasy.ch
ncbi.nlm.nih.gov

I do hope this helps,

R:)




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