From: Alexander Sczyrba <asczyrba@willa.rockefeller.edu>
To: mgreese@lbl.gov
CC: asczyrba@willa.rockefeller.edu
Subject: MAGPIE References
Date: Thu, 22 Jul 1999 13:38:25 -0400 (EDT)


Hi Martin,

here are the references you asked for:

1) MAGPIE

The new (eukaryotic) MAGPIE version will be presented as poster
"Multigenome MAGPIE" at ISMB'99...

Gaasterland, T. & Ragan, M. (1998).
Constructing multi-genome views of whole microbial genomes.
Journal of Microbial and Comparative Genomics, 3, 305--312.

Gaasterland, T. & Sensen, C. W. (1996).
Fully automated genome analysis that reflects user needs and
preferences --- a detailed introduction to the {MAGPIE} system architecture.
Biochimie, 78, 302--310.

2) Calypso

Calypso is an evolutionary genomics program under development (D. Field
unpublished).  Its primary function is to find repetitive regions in DNA
and protein sequences that have higher than average mutation rates.
Calypso simplifies and automates searching large amounts of sequence data
for evolutionary patterns involving repetitive sequences. Patterns are
found in input sequences (unlimited size and number of sequences) and can be
automatically blasted against user-specified databases. Calypso is written
in perl, interfaces with a variety of native unix programs, and presents
output in a variety of formats including html. For the Drosophila project
it was used to identify all perfect microsatellite repeats (mono- to
hexanucleotide repeats above thresholds of 14, 7, 4, 3, 2, and 2).


3) REPuter

S. Kurtz and C. Schleiermacher (1999):
REPuter: Fast Computation of Maximal Repeats in Complete Genomes
Bioinformatics, 15(5), 426-427

Genomes are scattered with repeats of various kinds and lengths.
Given a parameter l, REPuter determines all repeats of length l 
or above. REPuter's runtime is linear in the size of the
genome and in the size of the output. For suitable chosen l, complete
genomes can be analyzed in a matter of seconds.


  Alex