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