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These programs expect an alignment or sequences and try to find the best-conserved fragments within them:

  • Originally, the classical VISTA was used for this, with a cutoff of 70% identity over 100 bp.
  • UCSC's most conserved is based on coding regions. Covers 5% of the genome, no configurable threshold.
  • Genomic Evolutionary Rate Profiling (GERP) : is only available in perl and does not seem to be threshold-based, it's available on UCSC Encode though
  • MCS wants an alignment, a tree, genomic coordiantes for UCSC (bravo!), repeats and exons and a P-Value cutoff value. Nice, but only a webversion.
  • gumby expects somewhat less parameters and is downloadable in source (seems to be part of RankVista

Note: When in doubt, prefer multiple alignments (paper)