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Date: Mon, 23 Feb 1998 22:22:18 -0500
From: walker@sky (D Roland Walker)
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To: ncbi@sky
Subject: Seminar Tue 24 Feb
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SEALS, A System for Easy Analysis of Lots of Sequences
Tue, 24 Feb, 11:00 am.
Bldg. 38A, 8th floor 

Fully automated sequence analysis is not possible or desirable. 

SEALS (A System for Easy Analysis of Lots of Sequences) is designed
to facilitate semi-automatic sequence analysis at the genome scale,
leveraging human intelligence by simplifying laborious tasks, without 
taking human judgement out of the loop.

To this end, SEALS includes a large number of user-level commands,
which provide

  common file manipulations
  glue for other popular analysis programs
  Entrez retrieval
  GenBank flatfile manipulation
  fasta library filtering/sorting
  BLAST filtering/sorting
  access to the NCBI taxonomy
  etc.

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

In addition to providing user-level sequence analysis tools, SEALS also
aims to provide a rapid application 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 was written in Perl, for portability and ease of development.  I
will discuss the design and implementation of SEALS itself, and the 
design and implementation of several research projects using SEALS,
including 

 subtractive comparison of genomes
 similarity clustering of sequences at the domain level
 searching for analogous isozymes
 3-D fold recognition by sequence similarity

This is not a tutorial for users, though I will be happy to give one 
at a later date.

Roland