ArticlePLoS computational biology2016
GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
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- Disruption of the standard kinetochore in holocentricProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolutionary mechanisms underlying the diversification of nuclear factor of activated T cells across vertebrates.Scientific reports · 2023Article
- slag: A program for seeded local assembly of genes in complex genomes.Molecular ecology resources · 2022Article
- Salicylic acid fights against Fusarium wilt by inhibiting target of rapamycin signaling pathway in Fusarium oxysporum.Journal of advanced research · 2022Article
- Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS).Methods in molecular biology (Clifton, N.J.) · 2022Article
- Discovery of Early-BranchingFrontiers in microbiology · 2022Article
- Should we hail the Red King? Evolutionary consequences of a mutualistic lifestyle in genomes of lichenized ascomycetes.Ecology and evolution · 2022Article
- A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina.Mycorrhiza · 2022Article
- A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.Molecular ecology · 2021Article
- Insights into the genome and secretome of Fusarium metavorans DSM105788 by cultivation on agro-residual biomass and synthetic nutrient sources.Biotechnology for biofuels · 2021Article
- The complete molecular sequence of chloroplast genome ofMitochondrial DNA. Part B, Resources · 2021Article
- Extraordinary Sequence Diversity and Promiscuity of Centromeric Satellites in the Legume Tribe Fabeae.Molecular biology and evolution · 2020Article
- Direct visualization of degradation microcompartments at the ER membrane.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Population Genomic Analysis Reveals a Highly Conserved Mitochondrial Genome inFrontiers in microbiology · 2020Article
- Detecting Introgression Between Members of theFrontiers in microbiology · 2020Article
- STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data.BMC bioinformatics · 2019Article
- Tracking outbreak populations of the pepper weevil Anthonomus eugenii (Coleoptera; Curculionidae) using complete mitochondrial genomes.PloS one · 2019Article
- The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen.BMC evolutionary biology · 2018Article
- riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often neglected or poorly assembled, although they contain interesting information from phylogenetic or epidemiologic perspectives, but also single copy regions can be assembled. The program is capable of targeting multiple regions within a single run. Furthermore, GRAbB can be used to extract specific loci from NGS data, based on homology, like sequences that are used for barcoding. To make the assembly specific, a known part of the region, such as the sequence of a PCR amplicon or a homologous sequence from a related species must be specified. By assembling only the region of interest, the assembly process is computationally much less demanding and may lead to assemblies of better quality. In this study the different applications and functionalities of the program are demonstrated such as: exhaustive assembly (rDNA region and mitochondrial genome), extracting homologous regions or genes (IGS, RPB1, RPB2 and TEF1a), as well as extracting multiple regions within a single run. The program is also compared with MITObim, which is meant for the exhaustive assembly of a single target based on a similar query sequence. GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.