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Exploring Sequence Alignment Techniques in Bioinformatics: Global, Local, and Semi-Global Examples

This document presents an overview of various sequence alignment techniques used in bioinformatics, focusing on global, local, and semi-global alignment examples. Different scoring functions are applied, including match scores, substitution penalties, and indel values. The significance of initiating alignments, tracking maximum table values, and understanding local alignments are emphasized. The examples illustrate how to identify alignments using specific scoring systems and the importance of table values in tracing back for localized sequences.

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Exploring Sequence Alignment Techniques in Bioinformatics: Global, Local, and Semi-Global Examples

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  1. Sequence Alignment Examples Fall 2003 Dr. Susan Bridges Department of Computer Science and Engineering Bioinformatics

  2. Global Alignment Example • Different scoring functions can be used with any of the algorithms. • For this example, use the following scoring function: • Indel (add a space) -2 • Match +2 • Substitution -1 Department of Computer Science and Engineering Bioinformatics

  3. Global Alignment Result A A C C C T A A G C C T T _ | | | | | | | Department of Computer Science and Engineering Bioinformatics

  4. Local Alignment • For this example, use the following scoring function: • Indel (add a space) -2 • Match +2 • Substitution -1 • A zero entry stops a local alignment so it is not necessary to keep track of the source of 0 entries Department of Computer Science and Engineering Bioinformatics

  5. Finding Local Alignments • There may be several local alignments • Each local alignment begins from the largest value in the table and works back to a value of 0. • Symbols after the last non-zero entry (working backward) and before the maximum value (working backward) are not considered to be aligned. Department of Computer Science and Engineering Bioinformatics

  6. Local Alignment Result A A C C C T A _ A G C C T T | | | | | Department of Computer Science and Engineering Bioinformatics

  7. Semi-Global Alignment • For this example, use the following scoring function and global procedure: • Indel (add a space) -2 • Match +2 • Substitution -1 • Initialize first row to 0’s • Select largest value in border row and column (last row and last column) as beginning of alignment. Trace back from this value until encounter first row or first column. Department of Computer Science and Engineering Bioinformatics

  8. Semi Global Alignment A A G C C T G C C T T | | | | Department of Computer Science and Engineering Bioinformatics

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