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This document summarizes techniques for local sequence alignment using indexing and extensions. It discusses: 1. Indexing sequences with words or patterns of a fixed length k to initiate local alignments and improve sensitivity over simple word matching. 2. Extending local alignments by allowing gaps until the alignment score falls below a statistical threshold. 3. Methods to trade off sensitivity and speed, such as using multiple patterns, inexact words, or patterns with non-consecutive positions.

Author

Gongmyung Lee

Language

EN