Based on functional and evolutionary conservation, several stress-related candidate transcripts and transcription factors were identified.
In this study, we examined the relationship between protein conservation and promoter conservation in detail, by decomposing it based on functional categories.
Although the algorithms based on functional information (Gene Ontology terms/ protein domains) achieve better results than standard conservation-based approaches, a fair testing procedure is more difficult because the predictions can be biased toward more abundant functional classes.
Classifications are based on functional mobility.
Despite the acknowledged necessity of a phylogeny-based evaluation of orthology, thus far the majority of quality assessment tests are based on the functional conservation of predicted orthologs 18– 218
In a system such as the S. alburnoides complex, in which no genomic information is available, our strategy was to isolate potential candidates for sex determination and assess, based on their conservation, functional characteristics and expression patterns whether they could have a role in the establishment of the phenotypic sex.
For example, although Glimmer3.0 (Delcher et al., 2007) is often considered to have lower specificity than other predictors (e.g. GeneMark HMM or Prodigal), many genes predicted by Glimmer3.0 and not included in genome annotations have been confirmed in a recent analysis, based on evolutionary conservation and functional characterization (Wood et al., 2012).
Comparative genomic sequence analysis has proven to be a powerful tool for the identification of putatively functional sequences, predicting functional significance based on evolutionary conservation [ 9- 15].
Often gene functions of chicken genes were annotated based on sequence conservation without further functional evidence.
