ANNOUNCING A NEW EMAIL CAPABILITY FOR ANALYZING AMINO ACID SEQUENCES

James Freeman jfreeman at news.bu.edu
Mon Nov 27 18:30:42 EST 1995


ANNOUNCING A NEW EMAIL CAPABILITY FOR ANALYZING AMINO ACID SEQUENCES

The Protein Sequence Analysis (PSA) E-mail server, has been
IMPROVED. Two types of sequence analysis are now supported, and the
server can analyze amino acid sequences of any length upto 1000
residues. In addition, the server uses new models for alpha-beta
proteins containing central beta sheets or beta barrels.

The PSA is available for researchers who have amino acid sequences for
proteins of unknown structure and for which no homologous sequences
are known.  You send the server one amino acid sequence. The server
may be instructed to analyze the sequence in either of two ways: using
<em>type-1</em> or <em>type-2</em> DSMs.  (DSMs are Discrete
State-space Models for patterns of alpha-helices, strands, tight
turns, and loops in specific structural classes).

Type-1 models are for complete sequences from monomeric,
single-domain, globular, water-soluble proteins in several recognized
structural classes. They are also appropriate for those subsequences
of membrane-spanning proteins that are believed to extend beyond the
membrane (based on a hydropathy profile).
Type-2 models, in contrast, are for either partial or complete
sequences from potentially large proteins that violate one or more of
the modeling assumptions embodied in Type-1 models. For example,
Type-2 models are appropriate for proteins that have one or more of
the following properties: (1) they are multimeric; (2) they have more
than one structural domain; or (3) they are not globular or soluble
(e.g., membrane-spanning proteins).

The PSA server is maintained at the BioMolecular Engineering Research
Center of Boston University. For information on usage, send an empty
email message to psa-request at darwin.bu.edu with the word "help" in the
subject field.

The analysis algorithm is based on optimal filtering and smoothing
algorithms as described in the paper "Structural analysis based on
state-space modeling" by C.M. Stultz, J.V.  White, and T.F. Smith,
Protein Science (1993), 2, 305-314. The mathematical basis for the
models and algorithms is presented in "Protein Classification by
Stochastic Modeling and Optimal Filtering of Amino-Acid Sequences," by
J.V.  White, C.M.  Stultz, and T.F. Smith, Mathematical Biosciences
(1994), 119, 35-75.

--
Jim Freeman  P: mammon at tiac.net W: jfreeman at darwin.bu.edu
Programmer/Analyst at Bio-Molecular Engineering Center at BU
The last bug is not fixed until the last user is dead.
http://www.tiac.net/users/mammon/index.html





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