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Gramene Genomes 2005 Updates

Gramene Genomes 2005 Updates. Chengzhi Liang Gramene SAB meeting, San Diego, Jan 13, 2006. Overview. Data summary: Genomes: rice, Arabidopsis, maize Track data: Genes, Marker, EST, GSS, Array, FST Protein domains Synteny, orthologs System components:

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Gramene Genomes 2005 Updates

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  1. Gramene Genomes 2005 Updates Chengzhi Liang Gramene SAB meeting, San Diego, Jan 13, 2006

  2. Overview • Data summary: • Genomes: rice, Arabidopsis, maize • Track data: Genes, Marker, EST, GSS, Array, FST • Protein domains • Synteny, orthologs • System components: • Ensembl software, and Gramene pipeline • Functional modules: Genome Browser (including Compara), Blast, and GrameneMart • Current Ensembl version in Gramene: v30

  3. 2005 Updates • TIGR Assembly v3 • TIGR gene models, protein domain, GO associations, Fgenesh predictions • Arabidopsis browser: copy from NASC • Maize browser: for AGI BAC FPC map • Compara • Between rice, maize and Arabidopsis • GrameneMart • For search and download

  4. 2005 Updates (cont’d) • New Tracks on Rice Browser, e.g., • Rice TE • Array tracks: oligoes, SAGE tags, MPSS tags • SNPs between japonica and indica • FST for T-DNA and Ds • Wild rice BAC ends • EST clusters

  5. Rice SNP Track

  6. SNP Page

  7. MPSS Track

  8. External MPSS Site

  9. An Array Sequence Track

  10. PLEXdb Site

  11. Plan for 2006 • Add QTL/Gene track to rice browser • Integration of curated protein set with TIGR gene models • Add more sequences in maize browser • Upgrade to Ensembl 36 • Add more data to GrameneMart

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