Multiple genome alignment

In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate.

11p vioraclene 31-03-2024 4 2   Download

Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data.

10p viellison 28-03-2024 3 1   Download

Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type.

19p vialfrednobel 29-01-2022 7 1   Download

Distinguishing biological from technical variation is crucial when integrating and comparing single-cell genomics datasets across different experiments. Existing methods lack the capability in explicitly distinguishing these two variations, often leading to the removal of both variations.

28p viarchimedes 26-01-2022 5 0   Download

The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference.

12p vilarryellison 29-10-2021 20 1   Download

Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process.

11p vibeauty 23-10-2021 14 1   Download

Proteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast and effective framework to automatically identify functionally conserved proteins in a systematic way.

7p vijeeni2711 24-07-2021 11 0   Download

Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial role in plant response to various stresses by regulating the expression of stress-responsive genes.

13p vijeeni2711 24-07-2021 19 0   Download

The inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem.

14p viwyoming2711 16-12-2020 10 1   Download

All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes.

11p viwyoming2711 16-12-2020 18 1   Download

The k-mer counting problem, which is to build the histogram of occurrences of every k-symbol long substring in a given text, is important for many bioinformatics applications. They include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection.

12p viwyoming2711 16-12-2020 16 1   Download

Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. However, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes.

16p viwyoming2711 16-12-2020 10 1   Download

Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily related genomes in an integrated fashion, providing a basis for downstream analyses such as rearrangement studies and phylogenetic inference.

20p vikentucky2711 26-11-2020 11 1   Download

Identification of ortholog groups is a crucial step in comparative analysis of multiple genomes. Although several computational methods have been developed to create ortholog groups, most of those methods do not evaluate orthology at the sub-gene level.

16p vikentucky2711 26-11-2020 11 1   Download

Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accuracy of predicted gene structures has not been critically evaluated, mostly due to the scarcity of proper assessment methods.

13p vikentucky2711 26-11-2020 10 0   Download

The post-genomic era with its wealth of sequences gave rise to a broad range of protein residueresidue contact detecting methods. Although various coevolution methods such as PSICOV, DCA and plmDCA provide correct contact predictions, they do not completely overlap.

9p vioklahoma2711 19-11-2020 6 1   Download

Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny.

8p viconnecticut2711 28-10-2020 13 1   Download

Phylogenetic implication in bacterial genomics is important to understanding difficulties such as population history, antimicrobial resistance and transmission dynamics. It has been claimed that partial genome sequences would clarify phylogenetic relationships between isolated organisms, but up to now, no sustaining approach has been proposed to use competently these data. concatenation of sequences of different genes as well as building of consensus trees only consider the few genes that are shared among all organisms.

8p kequaidan2 11-12-2019 27 0   Download

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Simultaneous alignment of short reads against multiple genomes...

0p thulanh21 15-11-2011 31 1   Download

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Critical Care giúp cho các bạn có thêm kiến thức về ngành y học đề tài:Measuring the accuracy of genome-size multiple alignments...

11p thulanh19 05-11-2011 45 2   Download