October 1, 2007 (Vol. 27, No. 17)


Strong Points: Multiple approaches
Weak Points: Requires considerable knowledge to interpret

Another track toward “deciphering the code of gene regulation” is that taken by dcode.org’s Comparative Genomics Center. Here, the approach is multifaceted and comes in the form of several online applications. The first of these is to use genomic alignments. Two tools are available: ECR Browser (examines evolutionary conservation of multiple genomes) and Genome Alignment (aligns a FASTA nucleotide sequence to a genome of choice). Another approach uses identification of conserved transcription factor binding sites. Tools here include multiTF (multiple sequence alignments) and rVista (pairwise alignments). A third approach, regulation of coexpressed genes, is provided by the programs SynoR (vertebrate predictions) and Creme (coexpressed human genes). If you’re looking for a place to dump in a sequence and get out a result, you’ll probably be disappointed here, but multiple algorithms are probably essential for identifying regulatory elements, and in this regard, dcode stands up well.

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