The following is an excerpt from the chapter
Protein Identification and Analysis Tools in the ExPASy Server by Wilkins
et al.
published in the book
2-D Proteome Analysis Protocols (1998). Editor
A.J. Link. Humana Press, New Jersey.
The AACompSim tool [references] allows the theoretical AA composition of one protein in
the SWISS-PROT database to be compared to proteins from one or all species
in the database. This serves two main purposes. Firstly, to allow the
simulation of matching undertaken for identification purposes with
AACompIdent. Secondly, it allows the detection of weak
similarities between proteins by comparison of their compositions rather
than sequences, as explored by Hobohm and Sander (1).
Use of AACompSim
To use AACompSim, first select the constellation of amino acids you wish to
work with. If you wish to simulate matching undertaken with empirical data,
you should specify constellation 2. To match against the database for
detecting protein similarities, you should use all 20 amino acids in
constellation 0. Then specify an e-mail address to where the results can be
sent, the SWISS-PROT identification name (e.g. IPIA_TOBAC) or accession
number (e.g. Q03198) of the protein you would like to compare against the
database, and the SWISS-PROT abbreviation for the species to match against
(e.g. 'SALTY' for Salmonella typhimurium). If desired, matching can be done
against all species in the database by specifying 'ALL'. Finally, select
the 'Search' button to submit the match to ExPASy. AACompSim will return
three lists of proteins, similar to those from AACompIdent. A sample output
is shown in figure 6.
Comments
- AACompSim automatically uses the theoretical pI and MW of the specified
protein in the matching procedure. The pI and MW are calculated as in
Compute pI / MW .
- Default windows of pI ± 0.25 and MW ± 20% used by AACompSim in matching,
however matches undertaken without these windows are also included in the
program output.
References:
- Hobohm, U. and Sander, C. (1995) A sequence property approach to searching protein databases. J. Mol.
Biol. 251, 390-399.
Last modified 06/Nov/2001 by CHH
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