GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses.
The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.
Fredslund
Jakob
J
Bioinformatics Research Centre, University of Aarhus, Høegh-Guldbergsgade 10, 8000 Aarhus C, Denmark. jakobf@birc.au.dk
Madsen
Lene H
LH
Hougaard
Birgit K
BK
Sandal
Niels
N
Stougaard
Jens
J
Bertioli
David
D
Schauser
Leif
L
D001483:Base Sequence; D017124:Conserved Sequence; D017931:DNA Primers; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D007887:Fabaceae / Q000235:genetics*; D005819:Genetic Markers; D023281:Genomics / Q000379:methods; D020407:Internet; D006109:Poaceae / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
D017931:DNA Primers; D005819:Genetic Markers