A Design to Return All Local Sequence Alignments by Ed Wachtel

Author:Ed Wachtel [Wachtel, Ed]
Language: eng
Format: epub
Published: 2017-03-11T08:00:00+00:00

For example, if the w string is AGTAGACG, substring AGT is converted to 213. It is not found in the map. GTA becomes 132. It is found, vI=2 wI=1 is saved as a potential local alignment. substring TAG is not queried within the suffix map, since this substring is a part of the identified GTA potential local alignment.

The suffix map is unordered and therefore has constant access time. Each string v, w is traversed once. Thus, processing time is O(n).

Phase 2, potential local alignment expansion

A set of potential local alignments is passed from phase 1 to phase 2 for expansion in a forward and backward direction. The set is ordered by the index to v, followed by the index to w.

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