MacPattern v2.0 available

Rainer Fuchs Fuchs at EMBL-Heidelberg.DE
Mon Sep 14 08:04:51 EST 1992


The new version v2.0 of MacPattern is now available.

MacPattern is a Macintosh application which was originally designed for
protein pattern searches using the PROSITE pattern database.

Version 2.0 added the following new features:

- Support for Steven Henikoff's BLOCKS databases (Henikoff and Henikoff,
  Nucleic Acids Res. 19 (1991), 6565-6572).

  BLOCKS is a database of aligned protein fragments characteristic for
certain 
  protein families. These blocks are used by MacPattern for searches with 
  site-specific scoring matrices, thus complementing the standard PROSITE 
  consensus pattern searches approach.

  As for PROSITE, MacPattern displays a list of all entries in BLOCKS, and
a
  user can select the one (s)he wants to use. A simple click at an entry
  name in this list causes the complete database entry to be displayed, so 
  MacPattern can also be used as a convenient database browser.

  A full search of a 300+ protein sequence against all 2106 blocks in
BLOCKS 
  Release 5 takes about 8 minutes on a Macintosh IIcx.

- Statistical evaluation of protein sequences using general scoring schemes
  (Karlin and Brendel, Science 257 (1992), 39-49).

  This method was introduced by Karlin and Altschul (PNAS 87 (1990),
2264-2268) 
  to identify statistically significant segments in protein sequences. 
  MacPattern includes a set of scoring schemes described in recent
publications 
  by Karlin and colleagues, such as charge clusters, DNA-binding domains,
etc.,
  and allows the addition of new ones by the user.

Both new features require a great amount of floating-point operations.
Although MacPattern can be used on any Macintosh system, a Macintosh with a
mathematical co-processor is highly recommended!

Other changes in v2.0 include:

- Maximum number of entries allowed in Prosite or Blocks databases
increased 
  from 1,000 to 10,000.

- Entry names or accession numbers can be displayed in database browser
window.

- A couple of minor changes plus the inevitable bug fixes.


MacPattern can be obtained 

1) by electronic mail from netserv at embl-heidelberg.de:
   Get Mac_Software:macpattern.hqx

2) by anonymous ftp from ftp.embl-heidelberg.de:
   /pub/software/mac/macpattern.hqx

3) by electronic mail from the author (fuchs at embl-heidelberg.de)

4) on floppy disk from the author:
   Rainer Fuchs, EMBL Data Library, Postfach 10.2209, W-6900 Heidelberg,
Germany


Rainer Fuchs
EMBL Data Library
Fuchs at EMBL-Heidelberg.DE




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