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BLAST is a standard tool in bioinformatics for creating local sequencealignments using a "seed-and-extend" approach. Here we introduce an analogousseed-and-extend algorithm that produces local network alignments: BLANT, forBasic Local Alignment of Network Topology. This paper introduces BLANT-seed:given an input graph, BLANT-seed uses network topology alone to create alimited, high-specificity index of k-node induced subgraphs called k-graphlets(analogous to BLASTS's k-mers). The index is constructed so that, ifsignificant common network topology exists between two graphs, their indexesare likely to overlap. BLANT-seed then queries the indexes of two networks togenerate a list of common k-graphlets which, when paired, form a seed pair. Ourcompanion paper (submitted elsewhere) describes BLANT-extend, which "grows"these seeds to larger local alignments, again using only topologicalinformation.

BLANT: Basic Local Alignment of Network Topology, Part 1: Seeding local alignments with unambiguous 8-node graphlets