A local alignment tool for very long DNA sequences (original) (raw)
Journal Article
,
Search for other works by this author on:
,
1
National Center for Biotechnology Information, National Library of Medicine
NIH, Bethesda, MD 20894, USA
Search for other works by this author on:
,
1
National Center for Biotechnology Information, National Library of Medicine
NIH, Bethesda, MD 20894, USA
Search for other works by this author on:
Search for other works by this author on:
Accepted:
13 November 1994
PDF Cite
Kun-Mao Chao, Jinghui Zhang, James Ostell, Webb Miller, A local alignment tool for very long DNA sequences, Bioinformatics, Volume 11, Issue 2, April 1995, Pages 147–153, https://doi.org/10.1093/bioinformatics/11.2.147
Close
Navbar Search Filter Mobile Enter search term Search
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 Macintoshes, on PCs, and on DEC Alpha PCs. We also describe an application of sim2 for aligning long DNA sequences from Escherichia coli. sim2 facilitates contig-building by providing a complete view of the related sequences, so difference can be analyzed and inconsistencies resolved. Examples are shown using the alignment display and editing functions from the software tool ChromoScope.
This content is only available as a PDF.
© Oxford University Press
Citations
Views
Altmetric
Metrics
Total Views 43
3 Pageviews
40 PDF Downloads
Since 12/1/2016
| Month: | Total Views: |
|---|---|
| December 2016 | 2 |
| March 2017 | 1 |
| August 2017 | 1 |
| April 2018 | 1 |
| June 2020 | 1 |
| October 2020 | 1 |
| November 2020 | 3 |
| January 2021 | 2 |
| April 2021 | 1 |
| January 2023 | 1 |
| February 2023 | 1 |
| April 2023 | 2 |
| November 2023 | 2 |
| December 2023 | 4 |
| January 2024 | 4 |
| February 2024 | 1 |
| March 2024 | 4 |
| April 2024 | 2 |
| May 2024 | 1 |
| June 2024 | 2 |
| July 2024 | 3 |
| August 2024 | 1 |
| September 2024 | 1 |
| October 2024 | 1 |
×
Email alerts
Citing articles via
More from Oxford Academic