| | |
| | |
Stat |
Members: 3645 Articles: 2'506'133 Articles rated: 2609
26 April 2024 |
|
| | | |
|
Article overview
| |
|
Optimal Detection of Sequence Similarity by Local Alignment | Terence Hwa
; Michael Lassig
; | Date: |
6 Dec 1997 | Subject: | Statistical Mechanics; Biological Physics; Quantitative Methods | cond-mat.stat-mech physics.bio-ph q-bio.QM | Affiliation: | UC San Diego) and Michael Lassig (MPI Teltow | Abstract: | The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown to be characteristically different from that of gapless alignment. The optimal scores obtained for uncorrelated sequences obey certain robust scaling laws. Deviation from these scaling laws signals sequence homology, and can be used to guide the empirical selection of scoring parameters for the optimal detection of sequence similarities. This can be accomplished in a computationally efficient way by using a novel approach focusing on the score landscape. Furthermore, by assuming a few gross features characterizing the statistics of underlying sequence-sequence correlations, quantitative criteria are obtained for the choice of optimal scoring parameters: Optimal similarity detection is most likely to occur in a region close to the log side of the log-linear phase transition. | Source: | arXiv, cond-mat/9712081 | Services: | Forum | Review | PDF | Favorites |
|
|
No review found.
Did you like this article?
Note: answers to reviews or questions about the article must be posted in the forum section.
Authors are not allowed to review their own article. They can use the forum section.
browser Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
|
| |
|
|
|
| News, job offers and information for researchers and scientists:
| |