What Bioinformatics - Analyse und Management komplexer Systeme
What Bioinformatics - Analyse und Management komplexer Systeme
What Bioinformatics - Analyse und Management komplexer Systeme
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Sequence Comparison<br />
Similar, i.e. homologous, sequences have a similar structure and function.<br />
Typical task:<br />
• A relatively small newly sequenced genome has 1000 protein coding<br />
genes<br />
• Scan a database with 6 million entries for sequence similarity for<br />
each of the 1000 protein sequences<br />
(pairwise alignment allowing for gaps)<br />
For the gapped alignment of two sequences of length 100 there are<br />
more than 10 75 possible arrangements.<br />
Alignment by<br />
• Visual inspection (dot plots)<br />
• Dynamic programming (optimal alignment)<br />
• Heuristic methods (BLAST, FASTA)
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