GeMprospector

GeMprospector identifies cross-species genetic marker candidates and designs PCR primers from expressed sequence tags (ESTs) across legume and grass species to support genetic mapping, marker-assisted selection, and evolutionary studies.

Key Features:

• Automated primer generation: Automatically generates large sets of PCR primers based on conserved regions identified in sequence alignments.
• Multiple sequence alignment-based conserved exon detection: Detects conserved exons by performing multiple sequence alignments between submitted ESTs and homologous sequences.
• Intronic-region amplification: Designs primers targeting conserved exons to amplify flanking intronic regions for marker development.
• Database of homologous sequence clusters: Compares user-submitted ESTs to a database of homologous EST and genomic sequence clusters from legume and grass species.
• Cross-species marker development: Identifies conserved regions suitable for developing markers applicable across different species within legumes and grasses.

Scientific Applications:

• Genetic mapping: Provides PCR primers for markers useful in constructing genetic maps across species.
• Marker-assisted selection: Supplies cross-species genetic markers to support breeding and marker-assisted selection programs.
• Evolutionary and gene conservation studies: Enables investigation of evolutionary relationships and conserved genes among legumes and grasses.

Methodology:

Researchers submit collections of ESTs; GeMprospector performs multiple sequence alignments between submitted ESTs and homologous EST/genomic sequences in its database to identify conserved exons; primers are automatically designed to amplify intronic regions based on those alignments.