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mptrsen / Orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models
GNU General Public License v3.0
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Orthology is not established until the end of the analysis #1

Closed mptrsen closed 11 years ago

mptrsen commented 12 years ago

First, all the HMM searches are conducted, including the reciprocal BLAST search, if appropriate. The results are stored in the database. After that, orthology is established using a special SQL query. This way, I hope that the problem with one transcript being assigned to multiple genes (HMMs) will be void.

mptrsen commented 12 years ago

Working on it. However, I won't use a sophisticated query, it takes too long in the database. Instead, I'm gonna pull the whole results at the end of the analysis and do the sorting in Perl. Much cosier!

mptrsen commented 11 years ago

Got it. orthograph-reporter handles the SQL queries for establishing ortholog relationships.