Name
Abstract | ||
|---|---|---|
This paper presents a practical program, called sim2, for building local alignments of two sequences, each of which may be hundreds of kilobases long. Sim2 first constructs n best non-intersecting chains of ''fragments,'' such as all occurrences of identical 5-tuples in each of two DNA sequences, for any specified n ≥ 1. Each chain is then refined by delivering an optimal alignment in a region delimited by the chain. Sim2 requires only space proportional to the size of the input sequences and the output alignments, and the same source code runs on UNIX machines, on Macin- tosh, on PC, and on DEC ALPHA PC. We also describe an application of sim2 for aligning long DNA sequences from E. coli. Sim2 facilitates contig-building by provid- ing a complete view of the related sequences, so differences can be analyzed and inconsistencies resolved. Examples are shown using the alignment display and editing functions from the software tool, ChromoScope. |
Year | DOI | Venue |
|---|---|---|
1995 | 10.1093/bioinformatics/11.2.147 | Computer Applications in the Biosciences |
Keywords | Field | DocType |
dna sequence,source code,local alignment,linear space | Sequence alignment,Computer science,Source code,Unix,Algorithm,IBM PC compatible,Smith–Waterman algorithm,Computer program,Bioinformatics,Microcomputer,DEC Alpha | Journal |
Volume | Issue | ISSN |
11 | 2 | 0266-7061 |
Citations | PageRank | References |
12 | 3.80 | 7 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Kun-mao Chao | 1 | 838 | 94.05 |
| Jinghui Zhang | 2 | 27 | 15.36 |
| James Ostell | 3 | 1566 | 617.35 |
| W Miller | 4 | 1301 | 295.71 |