ANNOUNCEMENT: Pratt version 2.1

Inge Jonassen inge at brisk.ii.uib.no
Tue Feb 25 09:43:21 EST 1997


I am very pleased to announce 


                       Pratt version 2.1

            A tool for finding flexible patterns in 
                  unaligned protein sequences
                  
                          Written by: 
                         Inge Jonassen, 
                      Dept. of Informatics, 
                 University of Bergen, Norway

see also: http://www.ii.uib.no/~inge/Pratt.html

Source code (ANSI C) is available under this URL, and has been
compiled and run successfully on a variety of different UNIX
systems including LINUX.
                           
The author is very grateful to Des Higgins, John F. Collins, and Ingvar
Eidhammer for help and collaboration. Especially John F. Collins has 
proposed many of the features added in this version.

Pratt is a program that allows the user to efficiently search for
patterns conserved in a set of protein sequences. It allows the user
to define the class of patterns to be searched for, and then finds 
conserved patterns in this class. 

The time used by the program depends on 
- the set of sequences, 
- the class of patterns defined, 
- the minimum number of sequences a pattern is to match, 
- if an alignment or a query sequence is given, and
- the greediness of the search.

Version 2.0 was the last major version of Pratt, in the 2.1 version 
relatively minor things have been added/changed. 


New features in version 2.1 includes:
------------------------------------

- When showing the sequence segments matching each pattern, the sequence 
  symbols matching non-wildcard positions (components) in the pattern, 
  are written in upper-case while sequence symbols matching wild-cards 
  are in lower-case. Also, gaps (-) are added to align the symbols
  matching each pattern component. 

- Summary information about where the patterns match in the sequences is 
  written horizontally or vertically. 

- The user can restrict where in the sequences patterns should be looked
  for. This can be useful for example if the user knows some constraints 
  on the position of the patterns in one or more of the sequences. 
  
- A few bugs in version 2.0 have been fixed in 2.1. 

- Command line search control -- the user can now choose values for 
  all parameters that are in the menu directly from the command line. 
  This makes it quicker for experienced user to specify his/her search, 
  and also makes it easier to call Pratt from inside other programs. 
  
- The menu has been changed - two-letter commands are used.

- When using Pratt interactively (using the menu), some summary
  information about the search parameters will be shown after the user 
  asks the search to be started, and the user is given the opportunity 
  to go back to the menu to change parameter values.  

- On-line help is available from the menu by typing "help <option>"
  where option is one of the options in the menu or help for general help
  about Pratt. 
  
- When using Pratt interactively (using the menu), some summary
  information about the search parameters will be shown after the user asks 
  the search to be started, and the user is given the opportunity to go back 
  to the menu to change parameter values.



What was new in Version 2.0:
---------------------------

- heuristics and branch-and-bound has been implemented speeding the
  pattern search significantly especially for sets of relatively similar
  sequences (using special parameters the search will be guaranteed).

- A multiple sequence alignment (Clustal W format) of a subset of the 
  sequences can be input to Pratt, and used to restrict the search to 
  patterns consistent with the alignment

- A special "query" sequence (Fasta format) can be input, and Pratt will
  only search for patterns matching this. Makes it convinient to use
  Pratt together with database homology search programs.

- DNA sequences can be analysed (complementary strand not included in
  analysis).


Availability:
------------

  The program has been implemnted in ANSI C. It has been compiled and
  run on different UNIX workstations, DEC alpha, Sun, Silicon Graphics,
  and also on Linux PC's (Pentium and DEC alpha).
  
  The source code is available on:
  ftp://ftp.ii.uib.no/pub/bio/Pratt/Pratt2.1.tar
  
  For documentation and more information, see
  http://www.ii.uib.no/~inge/Pratt.html



References:
----------

  "Finding flexible patterns in unaligned protein sequences"
  Jonassen, I., Collins, J. F., Higgins, D. G.
  Protein Science (1995) 4:1587-1595.

  "Efficient discovery of conserved patterns using a pattern graph."
  Jonassen, I.
  Submitted to CABIOS.


If you want to be informed about bug fixes, new versions etc.,
send an email to inge at ii.uib.no. Bug reports, suggestions for
improvements etc. are sent to the same adress.


Sincerely,

Inge Jonassen, 
Dept. of Informatics,
University of Bergen,
HIB,
N5020 BERGEN,
Norway

email: inge at ii.uib.no




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