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 S. Kamoun for communicating unpublished results.
|Title of host publication||Nematology Symposium abstracts|
|Place of Publication||Leiden|
|Publisher||Brill Academic Publishers|
|Publication status||Published - 2002|