Generally, all types of biological sequence
comparison exploit the sequence alignment based on a dynamic programming approach.
(2011) Parallel Processing of Multiple Pattern Matching Algorithms for Biological Sequences
: Methods and Performance Results.
Bader, "A tile-based parallel Viterbi algorithm for biological sequence
alignment on GPU with CUDA," Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010 IEEE International Symposium on, vol., no., pp.1,8, 19-23 April 2010.
The course of action for a fast exact pattern matching algorithm for biological sequences
is the same as FS algorithm .
(2010) "A Hardware Accelerator for the Fast Retrieval of DIALIGN Biological Sequence
Alignments in Linear Space", IEEE Transactions on Computers, 59(6): 808-821.
SeqPup, a biological sequence
editor and analysis program for Macintosh computers.
While custom in-house code will be written for these large data searches, TGen reports that benchmarks were run on the National Center for Biotechnology Information (NCBI) BLAST (Basic Local Alignment Search Tool), an algorithm for comparing primary biological sequence
information, ClustalW, a general purpose multiple sequence alignment program for DNA or proteins, and NAMD, a parallel molecular dynamics code for large biomolecular systems.
Compiled from 15 assembled resources including GenBank, RefSeq, Entrez Gene and UniProtKB/Swiss-Prot, BONDplus allows researchers to move beyond the genome and leverage publicly available biological sequence
data, BINDplus biomolecular interaction data as well as GENESEQ, a value added database of patented biological sequences
The nodes of an abstract syntax tree are used to generate a suffix tree and we use the same methods on the suffix tree that have been successfully applied to biological sequence
matching to search for duplicate sections of code.
Training is designed for educators, principal investigators, postdoctoral fellows, graduate and advanced undergraduate students, and others in the life sciences who work with biological sequence
"You could design a series of [particles] that can latch onto a biological sequence
," Mirkin says.
and work with software for analysis of biological sequence