[ANNONCE] SEALS version 0.82

Roland Walker walker at ncbi.nlm.nih.gov
Wed Apr 22 16:21:57 EST 1998


Announce: SEALS version 0.82

Adapted from the SEALS home page at

  http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html

You may want to go there directly to read this with hyperlinks.

----------------------------------------------------------------------


Abstract
--------

  SEALS (A System for Easy Analysis of Lots of Sequences) is a software
  package expressly designed for large-scale research projects in bio-
  informatics.  Using a friendly, scalable command-line user interface,
  SEALS provides dozens of commands to help the user quickly implement
  standard sequence analysis protocols, design new investigations, and
  generally Get Things Done with dispatch.


Philosophy
----------

  SEALS is not an automated system for genome analysis.  That is not
  possible or desirable. SEALS is designed toward a different goal: to
  facilitate large-scale _semi-automatic_ sequence analysis projects,
  leveraging human intelligence by simplifying laborious tasks, without
  taking human judgment out of the loop.

  Graphical interfaces are avoided, as they tend to be slow and do not
  scale well.  Simple human-readable file formats are used exclusively
  in order to facilitate human interaction at every stage of a process.

  In addition to providing user-level sequence analysis tools, SEALS
  also aims to provide a rapid development environment, implementing
  a set of primitives at the appropriate level of abstraction for
  current research projects in sequence analysis.  New applications
  can be rapidly prototyped and non-programmers can easily create and
  modify novel functions using shell scripts.


Functionality
-------------

  SEALS includes such functions as

      Entrez retrieval
         Local database lookups are seamlessly integrated with remote
         NCBI Entrez retrievals for maximum speed.  The HTTP-based
         Entrez retrieval supports SSL for secure transactions.

      Taxonomy analysis
         SEALS tools understand the complete NCBI taxonomy. It is
         possible to filter lists of sequences according to any
         taxonomic criterion, allowing queries such as "What is the
         best eukaryotic BLAST hit for my favorite sequence?".

      Pattern matching
         Using Perl regular expressions in combination with Perl code
         snippets, SEALS tools can match and score arbitrarily complex
         patterns and specifications in sequences such as "tryptophan
         followed by a strongly hydrophobic region in the C-terminal
         end of a serine-rich protein".

      Scripting tools
         Robust scripters for popular programs such as BLAST and
         ClustalW provide conveniences for large-scale jobs along with
         a consistent user interface.

      BLAST parsers
         Any flavor of BLAST output, including the new PSI-BLAST, can
         be used with SEALS BLAST manipulation tools.  Recognition of
         file formats is automatic and transparent.

      Miscellaneous tools
         Dozens of useful general widgets are provided, including file-
         format converters, flatfile parser, fasta record sorter,
         DNA<->aa translation, Netscape interface, etc.

      Enhancements to standard Unix command-line functionality,
      including
         - unlimited-size fileglobs
         - recursive fileglobs
         - use of URLs as input filenames


 Complete documentation can be found at

       http://www.ncbi.nlm.nih.gov/Walker/SEALS/info/documentation.html



Implementation
--------------

  SEALS is written entirely in Perl.


Requirements
------------

  A Unix system that can run Perl.

  SEALS has been developed and tested on Solaris 2.6 and Irix 6.2 .
  It should be portable to any Unix system, including (in theory)
  Windows NT under the GNU-Win32 free Unix emulation environment.  (The
  NT port hasn't been tested).

      150 MB disk space is required for SEALS itself.  3 - 3.5 GB disk
      space is required for a complete recommended installation of
      external software and databases to use with SEALS.

      See the file install/README in the distribution for more
      information.

      SEALS works with the following external software:

         NCBI Toolkit  (principally BLAST-GP)
         Washington University BLAST
         Netscape 3.x or 4.04+
         SEG
         SignalP
         PHD
         HMMER
         CLUSTALW
         agrep
         gzip


      Though no single item (except gzip) is strictly necessary to run
      SEALS you'll want to at least have BLAST and SEG.  SEALS can
      download and install current versions of NCBI BLAST and Washington
      University BLAST automatically.


Availability
------------

  SEALS is free software, released into the public domain.

  Version 0.82 is available for download.


Publications
------------

  You can read a paper describing SEALS

    Walker, DR, and Koonin, EV (1997) SEALS: A System for Easy Analysis
    of Lots of Sequences. Intelligent Systems for Molecular Biology
    5:333-339.

  at

    http://www.ncbi.nlm.nih.gov/Walker/articles/SEALS.html

  though it is a bit out of date.

  An article for Bioinformatics (formerly CABIOS) is in preparation.


Notes
-----

  This is experimental research software, supported only by the author.
  It is not officially supported by the National Center for
  Biotechology Information (NCBI).

  The version number (0.82) is meant to remind you that this is beta
  software, still under development.


Please email me with any questions.

Roland Walker
walker at ncbi.nlm.nih.gov




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