Abstract:
parameters 3,10,13 of the scoring system employed, and is therefore more informative than a raw score for describing the quality of an alignment. Masking regions of restricted composition Many DNA and protein sequences contain regions of highly restricted nucleic acid and amino acid composition and regions of short elements repeated many times 15. The standard alignment models and scoring systems were not designed to capture the evolutionary processes that led to these low-complexity regions.As a result, two sequences containing compositionally biased regions can receive a very high similarity score that reflects this bias alone. For many purposes, these regions are uninteresting and can obscure other important similarities. Therefore, programs that filter low-complexity regions from query or database sequences will often turn a useless database search into a valuable one 15. Multiple sequences Global and local pairwise sequence comparison and alignment can be generalized to multiple sequences. From multiple alignments, profiles [related to hidden Markov models (HMMs)] can be abstracted and these can greatly enhance the sensitivity of database search methods to evolutionarily distant and subtle sequence relationships 11. As discussed by Sean Eddy on pp. 15–18 and by Kay Hofmann on pp. 18–21, this area is increasingly becoming the focus of algorithm and database development for biological sequence comparison. Dedication
Citations
| 1 | Nucleic Acids Res – Altshul - 1997 |
