Efficient exact pattern-matching in proteomic sequences
This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A n...
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| Formato: | bookPart |
| Idioma: | eng |
| Publicado em: |
2011
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| Texto completo: | http://hdl.handle.net/10198/4386 |
| País: | Portugal |
| Oai: | oai:bibliotecadigital.ipb.pt:10198/4386 |
| Resumo: | This paper proposes a novel algorithm for complete exact pattern-matching focusing the specificities of protein sequences (alphabet of 20 symbols) but, also highly efficient considering larger alphabets. The searching strategy uses large search windows allowing multiple alignments per iteration. A new filtering heuristic, named compatibility rule, contributed decisively to the efficiency improvement. The new algorithm’s performance is, on average, superior in comparison with its best-rated competitors. |
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