Efficient algorithms for regular expression constrained sequence alignment.
Yun Sheng ChungChin Lung LuChuan Yi TangPublished in: Inf. Process. Lett. (2007)
Keyphrases
- sequence alignment
- regular expressions
- pattern matching
- query language
- pairwise
- finite automata
- protein sequences
- dynamic programming
- gpu accelerated
- semistructured data
- amino acids
- deterministic finite automata
- xml schema
- binding sites
- phylogenetic analysis
- high level
- matching algorithm
- string matching
- multiple sequence alignment
- comparative genomics
- secondary structure
- query evaluation
- co occurrence
- data warehouse
- semistructured databases