Fair evaluation of global network aligners.

ABSTRACT:

Background

Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species. Then, function can be transferred from well- to poorly-annotated species between aligned network regions. Network alignment typically encompasses two algorithmic components: node cost function (NCF), which measures similarities between nodes in different networks, and alignment strategy (AS), which uses these similarities to rapidly identify high-scoring alignments. Different methods use both different NCFs and different ASs. Thus, it is unclear whether the superiority of a method comes from its NCF, its AS, or both. We already showed on state-of-the-art methods, MI-GRAAL and IsoRankN, that combining NCF of one method and AS of another

SUBMITTER: Crawford J 

PROVIDER: S-EPMC4460690 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature