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Practical Innovation at BioCon 2003

Poster Session

In Silico Identification of Candidate Single Nucleotide Polymorphism in Model Organisms

By Victor Guryev
Dr., Hubrecht Laboratory

Sequence data from public domain such as expressed sequence tags (EST) and whole genome sequencing (wgs) projects were explored to reveal candidates SNPs using search for nearly exact homology. The candidate SNPs were annotated with strain information, restriction endonuclease site affected, scored for homology degree, basecalling quality, aminoacid replacement and deposited in a publicly available database which can be accessed at http://rat.niob.knaw.nl. The project is tightly linked with other public databases such as Genbank, UniGene, LocusLink and EST/wgs projects and enables search of candidate SNPs by their IDs/accessions, gene name, map position, etc. Candidate SNPs data based on EST sequences can be automaticly piped to GENOTRACE (http://rat.niob.knaw.nl/genotrace) for building local genome assembly, determination of exon/intron structure, and oligonucleotide primer construction for genomic PCR amplification. Currently, the database comprises model organisms like zebrafish (Danio rerio, >1,700,000 entries) in order to facilitate mapping projects and rat (Rattus norvegicus, >84, 000 entries) to help discovering amino acid replacing SNPs or polymorphisms between different strains that may account for phenotypic differences. Experimental verification of a subset of candidate SNPs, incorporation of a score based on prediction of SNP effect on protein structure/function, and enlargement of database to cover other model organisms are in progress.

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