Determining Orthology

Reciprocal BLAST

• Reciprocal BLAST is a common computational method for predicting putative orthologues.
• Reciprocal BLAST is done by taking a fly gene and BLASTing it to a database of gene sequence from your organism of interest. The highest-scoring gene is taken and BLASTed to a database of fly gene sequence. If this returns the fly gene originally used as the highest scorer, then the two genes are considered putative orthologues.
• Of course, this does not prove orthology. Only experiment evidence can do that.
• Also, reciprocal BLAST does not fully take into account situtations where the gene history is complicated with gene duplications.
• Because of the availability of resources such as Homologene and InParanoid, it is not always necessary to do reciprocal BLAST yourself.

Homologene

• Homologene is a database of putative orthologues from NCBI derived from a method similar to reciprocal BLAST.
• Homologene data is available as a display column in the list of hits.

InParanoid

• InParanoid is another database of putative orthologues derived from a method similar to reciprocal BLAST. It will sometimes give slightly different answers than Homologene.
• InParanoid data is available as a display column in the list of hits.