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In recent years, several multiple network alignment methods have been developed.
A multiple network alignment algorithm must thus efficiently identify a biologically appropriate mapping between the genes.
For multiple network alignment experiments, PINALOG was excluded as the algorithm can only handle pairwise alignments.
Recently, a number of multiple network alignment algorithms have been proposed [ 12- 14].
Further directions for research include extending this approach to multiple network alignment and to network querying.
IsoRankN is an extension of IsoRank and mainly for multiple network alignment.
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However, to find multiple network alignments, IsoRank uses these scores in a time-intensive greedy algorithm.
Nevertheless, the Graemlin algorithm was the first algorithm capable of performing scalable, multiple network alignments [ 39].
The newer version, Graemlin 2.0 [ 40], is a global alignment algorithm that can adjust scoring function parameters and perform multiple network alignments.
With the novel representation of a layered alignment graph, NetworkBLAST-M can achieve dramatic reductions in run time and memory requirements for multiple network alignments.
Additionally, it may be possible to modify the star spread to account for existent gold standard network homology data, yielding even higher fidelity multiple network alignments.
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