scholarly journals WDSPdb: an updated resource for WD40 proteins

2019 ◽  
Vol 35 (22) ◽  
pp. 4824-4826 ◽  
Author(s):  
Jing Ma ◽  
Ke An ◽  
Jing-Bo Zhou ◽  
Nuo-Si Wu ◽  
Yang Wang ◽  
...  
Keyword(s):  
Web Site ◽  
Large Family ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Wd40 Repeat ◽  
Tertiary Structures ◽  
Cellular Processes ◽  
1000 Genomes ◽  
Repeat Proteins ◽  
The Web

AbstractSummaryThe WD40-repeat proteins are a large family of scaffold molecules that assemble complexes in various cellular processes. Obtaining their structures is the key to understanding their interaction details. We present WDSPdb 2.0, a significantly updated resource providing accurately predicted secondary and tertiary structures and featured sites annotations. Based on an optimized pipeline, WDSPdb 2.0 contains about 600 thousand entries, an increase of 10-fold, and integrates more than 37 000 variants from sources of ClinVar, Cosmic, 1000 Genomes, ExAC, IntOGen, cBioPortal and IntAct. In addition, the web site is largely improved for visualization, exploring and data downloading.Availability and implementationhttp://www.wdspdb.com/wdsp/ or http://wu.scbb.pkusz.edu.cn/wdsp/.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

2020 ◽  
Vol 36 (Supplement_1) ◽  
pp. i75-i83 ◽  
Author(s):  
Alla Mikheenko ◽  
Andrey V Bzikadze ◽  
Alexey Gurevich ◽  
Karen H Miga ◽  
Pavel A Pevzner
Keyword(s):  
Quality Assessment ◽  
Chromosome Segregation ◽  
Tandem Repeats ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Assembly Quality ◽  
Cellular Processes ◽  
Long Reads ◽  
Long Read ◽  
Eukaryotic Genomes

Abstract Motivation Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there are no tools for their quality assessment. Moreover, since the mapping of error-prone reads to ETRs remains an open problem, it is not clear how to polish draft ETR assemblies. Results To address these problems, we developed the TandemTools software that includes the TandemMapper tool for mapping reads to ETRs and the TandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that TandemTools not only reveals errors in ETR assemblies but also improves the recently generated assemblies of human centromeres. Availability and implementation https://github.com/ablab/TandemTools. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Kmer-db: instant evolutionary distance estimation

2018 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Adam Gudys ◽  
Maciej Dlugosz ◽  
Marek Kokot ◽  
Agnieszka Danek
Keyword(s):  
Data Structure ◽  
Web Site ◽  
Parallel Implementation ◽  
Evolutionary Relationship ◽  
Distance Estimation ◽  
Evolutionary Distance ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Efficient Data ◽  
Evolutionary Distance Estimation

AbstractSummaryKmer-db is a new tool for estimating evolutionary relationship on the basis of k-mers extracted from genomes or sequencing reads. Thanks to an efficient data structure and parallel implementation, our software estimates distances between 40,715 pathogens in less than 4 minutes (on a modern workstation), 44 times faster than Mash, its main competitor.Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site

scholarly journals Haplotype-aware graph indexes

2019 ◽  
Author(s):  
Jouni Sirén ◽  
Erik Garrison ◽  
Adam M Novak ◽  
Benedict Paten ◽  
Richard Durbin
Keyword(s):  
Genetic Variation ◽  
Precision Medicine ◽  
Chromosome 17 ◽  
Supplementary Information ◽  
Whole Genome ◽  
Supplementary Data ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Burrows Wheeler Transform ◽  
Haplotype Information

Abstract Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are non-biological, unlikely recombinations of true haplotypes. Results We augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows–Wheeler transform. We demonstrate the scalability of the new implementation by building a whole-genome index of the 5008 haplotypes of the 1000 Genomes Project, and an index of all 108 070 Trans-Omics for Precision Medicine Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes. Availability and implementation Our software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt and https://github.com/jltsiren/gcsa2. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable

2019 ◽  
Author(s):  
Michele Berselli ◽  
Enrico Lavezzo ◽  
Stefano Toppo
Keyword(s):  
Human Gene ◽  
State Of The Art ◽  
Comprehensive Analysis ◽  
Supplementary Information ◽  
Gene Promoters ◽  
Supplementary Data ◽  
Stem Loop ◽  
Hiv 1 ◽  
Rna And Dna ◽  
The Web

Abstract Motivation G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s, and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE. Results QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS respectively). While its assessment vs. known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2, and hTERT. Availability QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VCFShark: how to squeeze a VCF file

2020 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Agnieszka Danek
Keyword(s):  
Web Site ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Link Type ◽  
Order Of Magnitude ◽  
Better Than ◽  
De Facto Standards

AbstractSummaryThe VCF files with results of sequencing projects take a lot of space. We propose VCFShark squeezing them up to an order of magnitude better than the de facto standards (gzipped VCF and BCF).Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

scholarly journals GTShark: Genotype compression in large project

2018 ◽  
Author(s):  
Sebastian Deorowicz ◽  
Agnieszka Danek
Keyword(s):  
Web Site ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Link Type ◽  
Large Project ◽  
Supplementary Material

AbstractSummaryNowadays large sequencing projects handle tens of thousands of individuals. The huge files summarizing the findings definitely require compression. We propose a tool able to compress large collections of genotypes as well as single samples in such projects to sizes not achievable to date.Availability and Implementationhttps://github.com/refresh-bio/[email protected] informationSupplementary data are available at publisher’s Web site.

scholarly journals GTO: a toolkit to unify pipelines in genomic and proteomic research

2020 ◽  
Author(s):  
João R. Almeida ◽  
Armando J. Pinho ◽  
José L. Oliveira ◽  
Olga Fajarda ◽  
Diogo Pratas
Keyword(s):  
Next Generation Sequencing ◽  
Web Site ◽  
Life Sciences ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Next Generation ◽  
Modular Architecture ◽  
C Language ◽  
Proteomic Research ◽  
Generation Sequencing

AbstractSummaryNext-generation sequencing triggered the production of a massive volume of publicly available data and the development of new specialised tools. These tools are dispersed over different frameworks, making the management and analyses of the data a challenging task. Additionally, new targeted tools are needed, given the dynamics and specificities of the field. We present GTO, a comprehensive toolkit designed to unify pipelines in genomic and proteomic research, which combines specialised tools for analysis, simulation, compression, development, visualisation, and transformation of the data. This toolkit combines novel tools with a modular architecture, being an excellent platform for experimental scientists, as well as a useful resource for teaching bioinformatics inquiry to students in life sciences.Availability and implementationGTO is implemented in C language and it is available, under the MIT license, at http://bioinformatics.ua.pt/[email protected] informationSupplementary data are available at publisher’s Web site.

scholarly journals Haplotype-aware graph indexes

2019 ◽  
Author(s):  
Jouni Sirén ◽  
Erik Garrison ◽  
Adam M. Novak ◽  
Benedict Paten ◽  
Richard Durbin
Keyword(s):  
Genetic Variation ◽  
Chromosome 17 ◽  
Supplementary Information ◽  
Whole Genome ◽  
Supplementary Data ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Link Type ◽  
Supplementary Material ◽  
Haplotype Information

AbstractMotivationThe variation graph toolkit (VG) represents genetic variation as a graph. Although each path in the graph is a potential haplotype, most paths are nonbiological, unlikely recombinations of true haplotypes.ResultsWe augment the VG model with haplotype information to identify which paths are more likely to exist in nature. For this purpose, we develop a scalable implementation of the graph extension of the positional Burrows–Wheelertransform (GBWT). We demonstrate the scalability of the new implementation by building a whole-genome index of the 5,008 haplotypes of the 1000 Genomes Project, and an index of all 108,070 TOPMed Freeze 5 chromosome 17 haplotypes. We also develop an algorithm for simplifying variation graphs for k-mer indexing without losing any k-mers in the haplotypes.AvailabilityOur software is available at https://github.com/vgteam/vg, https://github.com/jltsiren/gbwt, and https://github.com/jltsiren/[email protected] informationSupplementary data are available.

scholarly journals MMseqs2 desktop and local web server app for fast, interactive sequence searches

2019 ◽  
Vol 35 (16) ◽  
pp. 2856-2858 ◽  
Author(s):  
Milot Mirdita ◽  
Martin Steinegger ◽  
Johannes Söding
Keyword(s):  
Protein Sequence ◽  
Response Times ◽  
Web Server ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Server Application ◽  
The Web

Abstract Summary The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2’s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST. Availability and implementation The app is easy to install for non-experts. GPLv3-licensed code, pre-built desktop app packages for Windows, MacOS and Linux, Docker images for the web server application and a demo web server are available at https://search.mmseqs.com. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals 6mA-Finder: a novel online tool for predicting DNA N6-methyladenine sites in genomes

2020 ◽  
Vol 36 (10) ◽  
pp. 3257-3259 ◽  
Author(s):  
Haodong Xu ◽  
Ruifeng Hu ◽  
Peilin Jia ◽  
Zhongming Zhao
Keyword(s):  
Molecular Mechanisms ◽  
Epigenetic Modification ◽  
Supplementary Information ◽  
Recursive Feature Elimination ◽  
Supplementary Data ◽  
Online Tool ◽  
Crucial Step ◽  
Cellular Processes ◽  
Multiple Cross ◽  
Species Specific

Abstract Motivation DNA N6-methyladenine (6 mA) has recently been found as an essential epigenetic modification, playing its roles in a variety of cellular processes. The abnormal status of DNA 6 mA modification has been reported in cancer and other disease. The annotation of 6 mA marks in genome is the first crucial step to explore the underlying molecular mechanisms including its regulatory roles. Results We present a novel online DNA 6 mA site tool, 6 mA-Finder, by incorporating seven sequence-derived information and three physicochemical-based features through recursive feature elimination strategy. Our multiple cross-validations indicate the promising accuracy and robustness of our model. 6 mA-Finder outperforms its peer tools in general and species-specific 6 mA site prediction, suggesting it can provide a useful resource for further experimental investigation of DNA 6 mA modification. Availability and implementation https://bioinfo.uth.edu/6mA_Finder. Supplementary information Supplementary data are available at Bioinformatics online.

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