TY - GEN

T1 - Inverse sequence alignment from partial examples

AU - Kim, Eagu

AU - Kececioglu, John

PY - 2007

Y1 - 2007

N2 - 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 different alignments. A rigorous way to compute parameter values that are appropriate for biological sequences is inverse parametric sequence alignment. Given a collection of examples of biologically correct alignments, this is the problem of finding parameter values that make the example alignments score close to optimal. We extend prior work on inverse alignment to partial examples and to an improved model based on minimizing the average error of the examples. Experiments on benchmark biological alignments show we can find parameters that generalize across protein families and that boost the recovery rate for multiple sequence alignment by up to 25%.

AB - 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 different alignments. A rigorous way to compute parameter values that are appropriate for biological sequences is inverse parametric sequence alignment. Given a collection of examples of biologically correct alignments, this is the problem of finding parameter values that make the example alignments score close to optimal. We extend prior work on inverse alignment to partial examples and to an improved model based on minimizing the average error of the examples. Experiments on benchmark biological alignments show we can find parameters that generalize across protein families and that boost the recovery rate for multiple sequence alignment by up to 25%.

UR - http://www.scopus.com/inward/record.url?scp=37249040464&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=37249040464&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-74126-8_33

DO - 10.1007/978-3-540-74126-8_33

M3 - Conference contribution

AN - SCOPUS:37249040464

SN - 9783540741251

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 359

EP - 370

BT - Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings

PB - Springer-Verlag

T2 - 7th International Workshop on Algorithms in Bioinformatics, WABI 2007

Y2 - 8 September 2007 through 9 September 2007

ER -