Alignment ambiguities

This article looks at some of these themes and includes: the need for alignment between supply chain strategy and the project concept; dealing with complexity, in particular the systematic and interrelatedness within project decisions; consideration of the ambiguity implicit in all major projects.

5p longtimenosee07 29-03-2024 6 2   Download

There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index.

16p vigalileogalilei 27-02-2022 10 1   Download

Read alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality.

12p vialfrednobel 29-01-2022 12 0   Download

Accurate discovery of somatic variants is of central importance in cancer research. However, count statistics on discovered somatic insertions and deletions (indels) indicate that large amounts of discoveries are missed because of the quantification of uncertainties related to gap and alignment ambiguities, twilight zone indels, cancer heterogeneity, sample purity, sampling, and strand bias.

25p viarchimedes 26-01-2022 8 0   Download

With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant calling, it has been found that a non-negligible proportion of the identified indel variants might be false positives due to sequencing errors, artifacts caused by ambiguous alignments, and annotation errors.

10p vikentucky2711 26-11-2020 11 0   Download

Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic fashion (fusion or intergenic trans-spliced RNAs).

11p vicoachella2711 27-10-2020 7 0   Download

This paper investigates the problem of speech separation from a mixture of two speech signals without source localization information in a room environment. Due to the lack of source information, the use of spatial detector comes at an expense of permutation ambiguity. To solve the problem, a permutation alignment algorithm based on correlation is employed to group the beamformer outputs into the correct sources.

11p dannisa 14-12-2018 27 1   Download

Word alignment has an exponentially large search space, which often makes exact inference infeasible. Recent studies have shown that inversion transduction grammars are reasonable constraints for word alignment, and that the constrained space could be efficiently searched using synchronous parsing algorithms. However, spurious ambiguity may occur in synchronous parsing and cause problems in both search efficiency and accuracy. In this paper, we conduct a detailed study of the causes of spurious ambiguity and how it effects parsing and discriminative learning. ...

5p hongdo_1 12-04-2013 30 3   Download

We study the challenges raised by Arabic verb and subject detection and reordering in Statistical Machine Translation (SMT). We show that post-verbal subject (VS) constructions are hard to translate because they have highly ambiguous reordering patterns when translated to English. In addition, implementing reordering is difficult because the boundaries of VS constructions are hard to detect accurately, even with a state-of-the-art Arabic dependency parser.

6p hongdo_1 12-04-2013 42 3   Download

From our earlier analysis, increasing controlling owners’ equity ownership beyond the minimum level needed for effective control creates incentive alignment effects that curtail entrenchment effects, which in turn increase earnings informativeness. On the other hand, the information argument suggests a negative relation between ownership concentration and earnings informativeness. As the incentive alignment and the information effects could coexist, the relation between ownership concentration and earnings informativeness is ambiguous and needs to be addressed empirically....

40p bin_pham 06-02-2013 52 4   Download