• How do I do a rat-specific BLAST analysis?
• How can I do DNA primer analysis?
• How can I do gene prediction with genomic sequence?

• Sequences, Maps
• Metagene, Primer Analysis, Primer3
• Blast

For more background information:

1. Genome Analysis, A laboratory manual, Vols 1-4: Mapping Genomes. Birren, etal. CSHL Press.
   Excellent lab manual describing genomic analysis, cloning and mapping techniques in humans and model organisms.
2. Modern Genetic Analysis, Griffiths, etal [online at NCBI]
   Textbook describing many fundamental analysis techniques

other online resources:

• NCBI BLAST tutorial, BLAST glossary

RGD has a BLAST tool available for public use. Several other sites also have tools for rat/rodent specific BLAST analysis.

• RGD BLAST- BLAST uses a heuristic algorithm to detect relationships among sequences which share regions of similarity.
• Rat Genome BLAST at NCBI - Blasts against a variety of rat genomic nucleotide and protein sequences
• BLAST at NCBI - Blasts against a wide variety of nucleotide and protein sequences, can be limited to sequences from a particular organism
• Rodent BLAST at MGD - Blast against Mouse/Rat sequences contained within NCBI or SwissProt

RGD has a basic PCR primer analysis utilities tool which does quick analysis tasks such as melting temperature calculation, translation, restricition analysis, etc.

For a more comprehensive primer analysis package, Primer3 at the Whitehead Institute is one of the leaders in primer design packages for genetic and genomic studies.

RGD provides a gene prediction tool, Metagene, which addresses this exact problem. The approach is novel in that the genomic sequence is submitted to a variety of sequence prediction engines and the results are combined by the analysis using a neural network algorithm to achieve the most accurate results.