๐”– Bobbio Scriptorium
โœฆ   LIBER   โœฆ

An optimization approach to multiple sequence alignment

โœ Scribed by F.Y. Hunt; A.J. Kearsley; Honghui Wan

Book ID
104349512
Publisher
Elsevier Science
Year
2003
Tongue
English
Weight
531 KB
Volume
16
Category
Article
ISSN
0893-9659

No coin nor oath required. For personal study only.

โœฆ Synopsis

The problem of multiple sequence alignment is recast ss an optimization problem using Markov decision theory. One seeks to minimize the expected or average cost of alignment subject to data-derived constraints.

In this setting, the problem is equivalent to a linear program which can be solved efficiently using modern interior-point methods. We present numerical results from an implementation of the algorithm for protein sequence alignment.

๐Ÿ“œ SIMILAR VOLUMES

Improving the divide-and-conquer approac
Improving the divide-and-conquer approach to sum-of-pairs multiple sequence alignment
โœ J. Stoye; S.W. Perrey; A.W.M. Dress ๐Ÿ“‚ Article ๐Ÿ“… 1997 ๐Ÿ› Elsevier Science ๐ŸŒ English โš– 419 KB

We consider the problem of multiple sequence alignment: given k sequences of length at most n and a certain scoring function, find an alignment that minimizes the corresponding "sum of pairs" distance score. We generalize the divide-and-conquer technique described in [1,2], and present new ideas on

An iterative structure-assisted approach
An iterative structure-assisted approach to sequence alignment and comparative modeling
โœ David F. Burke; Charlotte M. Deane; Hampapathalu A. Nagarajaram; Nuria Campillo; ๐Ÿ“‚ Article ๐Ÿ“… 1999 ๐Ÿ› John Wiley and Sons ๐ŸŒ English โš– 267 KB ๐Ÿ‘ 2 views

Correct alignment of the sequence of a target protein with those of homologues of known three-dimensional structure is a key step in comparative modeling. Usually an iterative approach that takes account of the local and overall structural features is required. We describe such an approach that expl