AACompSim Tool


The following is an (updated) 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 UniProtKB/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 UniProtKB/Swiss-Prot entry name (e.g. IPIA_TOBAC) or accession number (e.g. Q03198) of the protein you would like to compare against the database, and the UniProtKB/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

  1. 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 .
  2. 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:
  1. Hobohm, U. and Sander, C. (1995) A sequence property approach to searching protein databases. J. Mol. Biol. 251, 390-399.