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for communicating unpublished results.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 language | English |
|---|---|
| Title of host publication | Nematology Symposium abstracts |
| Place of Publication | Leiden |
| Publisher | Brill |
| Pages | 224 (289) |
| Volume | 4 |
| Publication status | Published - 2002 |