ESTScreen: identify secretory proteins in silico

Qin Ling, T.J.A. Borm, J. Bakker

Research output: Chapter in Book/Report/Conference proceedingAbstractAcademic

Abstract

The ever increasing gene sequences in databases offer unprecedented opportunity for biologists to exploit this new information source to ¿ nd answers to various biological questions. The collection of a great number of EST (expressed sequence tags) is a useful starting place for identifying secretory proteins involved in nematodeplant interactions, either in the form of pathogenicity factors or avirulent proteins which are targeted by host defence mechanisms. SignalP is a robust program generally used to identify signal peptides for secretion from protein sequences, but it is not suitable for analysing a large number of EST directly. To this end, we have developed and validated a software tool, ESTScreen, which automates screening of thousands of EST either through the SignalP web server or a standalone version. ESTScreen searches each cDNA sequence for a (user-de¿ ned) start codon, translates the sequence, submits automaticallyto SignalP and retrieves the output. ESTScreen then parses the SignalP prediction through a user-de¿ ned logical test and generates a FASTA ¿ le containing only EST encoding a signal peptide for secretion, which can be used in homology search and other subsequent analysis. This program can be a useful tool in the study of plant-pathogen interaction systems as well as other ¿ elds in which secreted molecules play important roles. The authors wish to thank Dr. S. Kamoun for communicating unpublished results.
Original languageEnglish
Title of host publicationNematology Symposium abstracts
Place of PublicationLeiden
PublisherBrill Academic Publishers
Pages224 (289)
Volume4
Publication statusPublished - 2002

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    Qin Ling, Borm, T. J. A., & Bakker, J. (2002). ESTScreen: identify secretory proteins in silico. In Nematology Symposium abstracts (Vol. 4, pp. 224 (289)). Brill Academic Publishers.