Comparative gene finder
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- Comparative gene finder search for term
Tool allowing gene prediction with additional information in the form of observed cross-species conservation. There is no ideal pair of genomes for cross-species gene finding, but the human-mouse pair (60-80 MYA) has often been used with reasonable success. Simple phylogenetics footprinting may not identify exons with great specificity. Modeling of sequence conservation is carried out using standrad models of molecular evolution, i.e. via phylogenetic trees and substitution rate matrices, easily implemented into GHMM-based systems (PhyloHMMs), or by pair HMM (PHMM) and their generalized cousins GPHLMMs which performs alignment and gene finding simultaneously. Regions between successive HSPs are called « banded ». (Edwards 2009)
