J Gouzy1, P Eugéne, E A Greene, D Kahn, F Corpet. 1. Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA/CNRS, Castanet-Tolosan, France. [mailto:fcorpet@toulouse.inra.fr]
Abstract
MOTIVATION: To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis. RESULTS: This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database. AVAILABILITY: XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.
MOTIVATION: To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis. RESULTS: This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database. AVAILABILITY: XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.
Authors: W C Nierman; T V Feldblyum; M T Laub; I T Paulsen; K E Nelson; J A Eisen; J F Heidelberg; M R Alley; N Ohta; J R Maddock; I Potocka; W C Nelson; A Newton; C Stephens; N D Phadke; B Ely; R T DeBoy; R J Dodson; A S Durkin; M L Gwinn; D H Haft; J F Kolonay; J Smit; M B Craven; H Khouri; J Shetty; K Berry; T Utterback; K Tran; A Wolf; J Vamathevan; M Ermolaeva; O White; S L Salzberg; J C Venter; L Shapiro; C M Fraser; J Eisen Journal: Proc Natl Acad Sci U S A Date: 2001-03-20 Impact factor: 11.205