Summary
Sequence Comparison: Summary
- Dynamic programming finds the optimal alignment between two sequences in a computing time proportional to NxM, where N and M are the sequence lengths
- Critical user choices include the scoring matrix, the gap penalties, and the algorithm (local, or global)
- FASTA and BLAST applies heuristics to speed up database search
- Statistics on local sequence alignments are defined by: raw score, bit score, E-values and P-values
- BLAST reports a "database" E-value, that takes into account the total number of residus in the sequence database