plant genome and systems biology group

Comparative Genomics Research

  • Simap

    SIMAP is a database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequences genomes.

  • mips-REdat

    The repeateElement database mips-REdat version9.0p contains currently around 42.000 sequences, with a focus on de novo detected LTR-retrotransposons from grass (~28.000) and other (~9.000) genomes hosted in PlantsDB. The repeat elements are classified by mips-REcat, a hierarchical repeats classification catalog, which facilitates data extraction at different levels of detail.

  • Regulomips

    Credo- Cis-Regulatory Element Detection Online- integrates the analysis and results of five algorithms widely used for the computational detection of conserved sequence motifs in noncoding sequences: AlignACE, DIALIGN, FootPrinter, MEME and MotifSampler.

  • MotifDB

    Detection of motifs significantly enriched for co-expressed gene groups (CEGs), GOslim categories and KEGG biochemical pathways (Berardini et al., 2004; at TAIR). Motifs are associated with co-expression and are derived from conserved regions within putative orthologous upstream sequences of Brassica oleracea and Arabidopsis thaliana.

  • COSmarker

    The Conserved Ortholog Sets are built iteratively by searching putative orthologs for the seed and each non-seed organism. If possible, use as seed a genome with full length proteins.

  • Analysis of syntenic regions

    CrowsNest is a perfect tool for this task.