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
