Results 1  10
of
407
Approximate pvalues for local sequence alignments
 Ann. Statist
, 2000
"... Siegmund and Yakir (2000) have given an approximate pvalue when two independent, identically distributed sequences from a nite alphabet are optimally aligned based on a scoring system that rewards similarities according to a general scoring matrix and penalizes gaps (insertions and deletions). The ..."
Abstract

Cited by 39 (1 self)
 Add to MetaCart
). The approximation involves an innite sequence of difculttocompute parameters. In this paper, it is shown by numerical studies that these reduce to essentially two numerically distinct parameters, which can be computed as onedimensional numerical integrals. For an arbitrary scoring matrix and afne gap penalty
Optimal alignments in linear space
 CABIOS
, 1988
"... Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed spacesaving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the newer proposals, bo ..."
Abstract

Cited by 292 (4 self)
 Add to MetaCart
, both in theory and in practice. The goal of this note is to give Hirschberg’s idea the visibility it deserves by developing a linearspace version of Gotoh’s algorithm, which accommodates affine gap penalties. A portable Csoftware package implementing this algorithm is available on the BIONET free
Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
 Computers and Chemistry
, 1996
"... In this paper, we borrow the idea of the Receiver Operating Characteristic (ROC) from clinical medicine and demonstrate its application to sequence comparison. The ROC includes elements of both sensitivity and specificity, and is a quantitative measure of the usefulness of a diagnostic. The ROC is u ..."
Abstract

Cited by 265 (5 self)
 Add to MetaCart
is used in this work to investigate the effects of scoring table and gap penalties on database searches. Studies on three families of proteins, 4Fe4S ferredoxins, lysR bacterial regulatory proteins, and bacterial RNA polymerase sigma factors lead to the following conclusions: Sequence families are quite
Ideal Gap Penalty
, 2006
"... Recall from previous lecture we can find the alignment between two DNA sequences by either performing global alignment using NeedlemanWunsch algorithm or local alignment using SmithWaterman algorithm. The method the two algorithms used to handle gaps is of particular interest. Thus far the strateg ..."
Abstract
 Add to MetaCart
the strategy is to add a fixed gap penalty when a gap occurs regardless what the alignment was for the previous nucleotide residue (see Figure 1). Below is the algorithm for calculating the alignment score based on linear gap penalty. This algorithm has both running time and space usage that is linear O
positionspecific gap penalties
, 1994
"... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, ..."
Abstract
 Add to MetaCart
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,
Support Vector Machines, Reproducing Kernel Hilbert Spaces and the Randomized GACV
, 1998
"... this paper we very briefly review some of these results. RKHS can be chosen tailored to the problem at hand in many ways, and we review a few of them, including radial basis function and smoothing spline ANOVA spaces. Girosi (1997), Smola and Scholkopf (1997), Scholkopf et al (1997) and others have ..."
Abstract

Cited by 189 (11 self)
 Add to MetaCart
noted the relationship between SVM's and penalty methods as used in the statistical theory of nonparametric regression. In Section 1.2 we elaborate on this, and show how replacing the likelihood functional of the logit (log odds ratio) in penalized likelihood methods for Bernoulli [yesno] data
Effects of gap open and gap extension penalties
, 2006
"... Abstract — Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence align ..."
Abstract

Cited by 2 (1 self)
 Add to MetaCart
Abstract — Fundamental to multiple sequence alignment algorithms is modeling insertions and deletions (gaps). The most prevalent model is to use gap open and gap extension penalties. While gap open and gap extension penalties are well understood conceptually, their effects on multiple sequence
PatternInduced Multisequence Alignment (PIMA) algorithm employing secondary structuredependent gap penalties for use in comparative protein modelling
, 1992
"... A multiple sequence alignment algorithm is described that uses a dynamic programmingbased pattern construction method to align a set of homologous sequences based on their common pattern of conserved sequence elements. This PatternInduced Multisequence Alignment (PIMA) algorithm can employ second ..."
Abstract

Cited by 80 (1 self)
 Add to MetaCart
secondarystructure dependent gap penalties for use in comparative modelling of new sequences when the threedimensional structure of one or more members of the same family is known. We show that the use of secondary structure information can significantly improve the accuracy of aligning structure
On Penalty and Gap Function Methods for Bilevel Equilibrium Problems
"... Abstract. We consider bilevel pseudomonotone equilibrium problems. We use a penalty function to convert a bilevel problem into onelevel ones. We generalize a pseudo ∇monotonicity concept from ∇monotonicity and prove that under pseudo ∇monotonicity property any stationary point of a regularized g ..."
Abstract

Cited by 3 (2 self)
 Add to MetaCart
Abstract. We consider bilevel pseudomonotone equilibrium problems. We use a penalty function to convert a bilevel problem into onelevel ones. We generalize a pseudo ∇monotonicity concept from ∇monotonicity and prove that under pseudo ∇monotonicity property any stationary point of a regularized
IS THERE A MOTHERHOOD PENALTY?: DECOMPOSING THE FAMILY WAGE GAP IN
, 2011
"... Decomposing the family wage gap in ..."
Results 1  10
of
407