[ANNONCE] SEALS version 0.82
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
You may want to go there directly to read this with hyperlinks.
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.
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.
SEALS includes such functions as
Local database lookups are seamlessly integrated with remote
NCBI Entrez retrievals for maximum speed. The HTTP-based
Entrez retrieval supports SSL for secure transactions.
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?".
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".
Robust scripters for popular programs such as BLAST and
ClustalW provide conveniences for large-scale jobs along with
a consistent user interface.
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.
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,
- unlimited-size fileglobs
- recursive fileglobs
- use of URLs as input filenames
Complete documentation can be found at
SEALS is written entirely in Perl.
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
SEALS works with the following external software:
NCBI Toolkit (principally BLAST-GP)
Washington University BLAST
Netscape 3.x or 4.04+
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.
SEALS is free software, released into the public domain.
Version 0.82 is available for download.
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
though it is a bit out of date.
An article for Bioinformatics (formerly CABIOS) is in preparation.
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.
walker at ncbi.nlm.nih.gov
More information about the Bio-soft