ProTeus (PROtein TErminUS) is a web-based tool for the identification of short linear signatures in protein termini. It is based on a position-based search method for revealing short signatures in termini of all proteins. The initial step in ProTeus development was to collect all signature groups (SIGs) based on their relative positions at the termini. The initial set of SIGs went through a sequential process of inspection and removal of SIGs, which did not meet the attributed statistical thresholds. The SIGs that were found significant represent protein sets with minimal or no overall sequence similarity besides the similarity found at the termini. These SIGs were archived and are presented at ProTeus. The SIGs are sorted by their strong correspondence to functional annotation from external databases such as GO. ProTeus provides rich search and visualization tools for evaluating the quality of different SIGs. A search option allows the identification of terminal signatures in new sequences. ProTeus (ver 1.2) is available at http://www.proteus.cs.huji.ac.il.
Bibliographical noteFunding Information:
We thank Noam Kaplan for his valuable suggestions and support. We thank the ProtoNet team for developing maintenance and support throughout. Special thanks to Alex Savenok for ProTeus web site design. Grant support is by the NoE European BioSapiens consortium. I.B. is supported by a fellowship of the SCCB, The Sudarsky Center for Computational Biology. Funding to pay the Open Access publication charges for this article was provided by the National Science Foundation under grant DBI-0218798 and the National Institutes of Health under grant HG02602-01.