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Table 1 Stage two algorithm

From: Optimal neighborhood indexing for protein similarity search

Algorithm 1 Stage 2
Ensure: reports if a matching key occurrence potentially belongs to an alignment
Require: query neighborhoods (leftquery and rightquery)
1: get database neighborhoods leftdb and rightdb
2: resultleft ← 0; highestleft ← 0
3: resultright ← 0; highestright ← 0
4: for i from 1 to L do
5:   resultleftresultleft + subst _score (leftdb [i], leftquery [i])
6:   if resultleft > highestleft then highestleftresultleft endif
7: end for
8: for i from 1 to L do
9:   resultrightresultright + subst _score(rightdb [i], rightquery [i])
10:   if resultright > highestright then highestrightresultright endif
11: end for
12: if highestleft + highestright ≥ threshold T MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaWenfgDOvwBHrxAJfwnHbqeg0uy0HwzTfgDPnwy1aaceaGae83eXtfaaa@376F@ then return true endif
13: return false