Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the auto-matic generation of high-quality alignments remains challenging. Since multiple alignments are usually employed at the very start of data

Automatic word alignment plays a critical role in statistical machine translation. Unfortunately the relationship between alignment quality and statistical machine translation performance has not been well understood. In the recent literature the alignment task has frequently been decoupled from

l findings are applicable to automatic database searches. Keywords: alignment quality analysis/evolutionary conservation/ genome analysis/protein sequence alignment/sequence space hopping Introduction Protein sequence alignments in twilight zone Protein sequences fold into unique three

protein family, or contain the given domain. The Hi " produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a

recognition, detection and clustering. The method is fast, does not require video alignment and is applicable in (but not limited to) many scenarios where the background is known. Moreover, we demonstrate the robustness of our method to partial occlusions, non-rigid deformations, significant changes in scale

for assessing the quality of alignments are highly requisite. Results: We present a statistical model-based alignment quality score. Unlike other quality scores, it does not require several par-allel alignments for the same set of sequences or additional structural information. Our quality score is based

examined systematically how linguistic information can be employed for word alignment improvement. In this paper, we present our experiments on finding out which linguistic information has which effect on word alignment quality, and we evaluate our experiments using precision and recall calculated

_SIM for a rate of false positives of 10%. Approxi-mately half of the improvement over the profile–profile com-parison methods is attributable to the use of profile HMMs in place of simple profiles. Alignment quality: Higher sensitivity is mirrored by an in-creased alignment quality. HHsearch produced 1.2, 1

Abstract Previous studies of the effect of word alignment on translation quality in SMT generally explore link level metrics only and mostly do not show any clear connections between alignment and SMT quality. In this paper, we specifically investigate the impact of word alignment on two pre

Automatic word alignment plays a critical role in statistical machine translation. Unfortunately, the relationship between alignment quality and statistical machine translation performance has not been well understood. In the recent literature, the alignment task has frequently been decoupled from