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» Multiple alignment by aligning alignments
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WABI
2007
Springer
123views Bioinformatics» more  WABI 2007»
14 years 1 months ago
Inverse Sequence Alignment from Partial Examples
When aligning biological sequences, the choice of parameter values for the alignment scoring function is critical. Small changes in gap penalties, for example, can yield radically ...
Eagu Kim, John D. Kececioglu
WABI
2004
Springer
106views Bioinformatics» more  WABI 2004»
14 years 22 days ago
Suboptimal Local Alignments Across Multiple Scoring Schemes
Abstract. Sequence alignment algorithms have a long standing tradition in bioinformatics. In this paper, we formulate an extension to existing local alignment algorithms: local ali...
Morris Michael, Christoph Dieterich, Jens Stoye
GECCO
2003
Springer
129views Optimization» more  GECCO 2003»
14 years 18 days ago
Evolutionary Two-Dimensional DNA Sequence Alignment
This article presents a model for DNA sequence alignment. In our model, a finite state automaton writes two-dimensional maps of nucleotide sequences. An evolutionary method for se...
Edgar E. Vallejo, Fernando Ramos
PPSN
2004
Springer
14 years 22 days ago
An Evolutionary Algorithm for the Maximum Weight Trace Formulation of the Multiple Sequence Alignment Problem
Abstract. The multiple sequence alignment problem (MSA) can be reformulated as the problem of finding a maximum weight trace in an alignment graph, which is derived from all pairw...
Gabriele Koller, Günther R. Raidl
RECOMB
2004
Springer
14 years 7 months ago
Aligning alignments exactly
d abstract) John Kececioglu and Dean Starrett Department of Computer Science The University of Arizona Tucson AZ 85721, USA A basic computational problem that arises in both the...
John D. Kececioglu, Dean Starrett