mips plant group

• 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

  mips Repeat Element database (mips-REdat) has been compiled from a variety of mainly public sources. The database is continuously extended by newly detected repeat elements from our pipeline and from updated repeat collections (see related links). To remove identical repeats the sequences are clustered to a non-redundant set with a 98% identity limit, taking the longest sequence as a representative.

  mips Repeat Element Catalog (mips-REcat) has been designed for automated repeat element annotation and flexible data retrieval. It integrates and extends existing repeat classifications into a systematic hierarchical tree structure.

• 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; www.arabidopsis.org 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.