Global alignment: Finding rearrangements during alignment
Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Director. Office of Science. Office of Biological and Environmental Research; National Science Foundation Graduate Fellowship (US)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 831112
- Report Number(s):
- LBNL-55262; R&D Project: LGFGAA; TRN: US200429%%1482
- Journal Information:
- Bioinformatics, Vol. 19, Issue Suppl. 1; Other Information: Journal Publication Date: 2003; PBD: 6 Jan 2003
- Country of Publication:
- United States
- Language:
- English
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