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パシフィコ横浜で開催された 第34回日本分子生物学会年回 でポスター発表をしました。発表は学会2日目の12月14日(水)でした。




GGRNA: fast and convenient universal search engine for genes and transcripts (2P-0113)

ABSTRACT: GGRNA (http://GGRNA.dbcls.jp/) is a powerful full-text search engine for transcripts archived in NCBI Reference Sequence (RefSeq) database. With one simple input field, GGRNA quickly searches RefSeq transcripts by various words and phrases including gene names, annotations, accession numbers, and even nucleotide sequences and amino acid sequences. In a search result, transcripts are grouped by gene locus if several transcript variants derived from alternative splicing are included in the result. GGRNA can search nucleotide sequences allowing one or two mismatches, and the query sequences may contain ambiguous nucleotides (N, R, Y, etc.). A typical nucleotide sequence search takes just one second, which dramatically enhances the usability of searching. Furthermore, we incorporated multiple databases such as Gene Ontology (GO) annotations, microarray probes and Reference Expression dataset (RefEx) into GGRNA by mapping their contents onto RefSeq transcripts and provided through a simple interface that can help users to easily find and browse relevant genes. For example, searches can be refined by adding GO terms to the queries; Microarray probe IDs are automatically converted into probe sequences and subjected as nucleotide sequence searches; An expression levels and patterns of each gene can be browsed using RefEx. We are planning to incorporate additional databases including PubMed, PDB, SNPs for further development. GGRNA currently searches RefSeq transcripts from human, mouse, rat, chicken, frog, zebrafish, fruit fly, worm, thale cress, rice, budding east and fission yeast. The web server should provide a wide range of applications for both ‘wet’ and ‘dry’ biologists.

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