Gene Network Homology in Prokaryotes Using a Similarity Search Approach: Queries of Quorum Sensing Signal Transduction
Figure 2
LMNAST operates in a BLAST-like manner, using the results of BLAST searches themselves as a curated database. 1. For each member of the query, in any nucleotide record, a homolog's membership to a character type is assigned by scoring below a specified BLAST E-value threshold. Genes assigned to characters are highlighted blue. Genes without sufficient homology to any character are represented by dashed boxes. 2. Sufficiently long stretches of adjacent characters are identified as seeds (red). 3. Sufficiently proximal characters are connected to seeds or seeds are connected to each other when separated by a base pair distance<d. 4. Rearrangements, losses, and deletions are scored according to a standard similarity heuristic. Noncontinuous elements are dropped iteratively until a maximum score is achieved, arriving at… 5. An LMNAST hit.