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Article ; Online: UniqTag: Content-Derived Unique and Stable Identifiers for Gene Annotation.

Jackman, Shaun D / Bohlmann, Joerg / Birol, İnanç

PloS one

2015 Volume 10, Issue 5, Page(s) e0128026

Abstract: When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. ... ...

Abstract	When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to ten builds of the Ensembl human genome spanning eight years to demonstrate this stability. The implementation of UniqTag in Ruby and an R package are available at https://github.com/sjackman/uniqtag sjackman/uniqtag. The R package is also available from CRAN: install.packages ("uniqtag"). Supplementary material and code to reproduce it is available at https://github.com/sjackman/uniqtag-paper.
MeSH term(s)	Genome, Human ; Humans ; Molecular Sequence Annotation/methods ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0128026
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Assembling genomes using short-read sequencing technology.

Jackman, Shaun D / Birol, Inanç

Genome biology

2010 Volume 11, Issue 1, Page(s) 202

Abstract: Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark. ...

Abstract	Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark.
MeSH term(s)	Animals ; Chromosome Mapping ; Computational Biology/methods ; Contig Mapping ; Genetic Techniques ; Genome ; Genome, Fungal ; Genome, Plant ; Humans ; Models, Genetic ; Pseudomonas/genetics ; Sequence Analysis, DNA/methods ; Ursidae/genetics ; Zea mays/genetics
Language	English
Publishing date	2010-01-28
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/gb-2010-11-1-202
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Article ; Online: UniqTag

Shaun D Jackman / Joerg Bohlmann / İnanç Birol

PLoS ONE, Vol 10, Iss 5, p e

Content-Derived Unique and Stable Identifiers for Gene Annotation.

2015 Volume 0128026

Abstract	When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to ten builds of the Ensembl human genome spanning eight years to demonstrate this stability. The implementation of UniqTag in Ruby and an R package are available at https://github.com/sjackman/uniqtag sjackman/uniqtag. The R package is also available from CRAN: install.packages ("uniqtag"). Supplementary material and code to reproduce it is available at https://github.com/sjackman/uniqtag-paper.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: ORCA: a comprehensive bioinformatics container environment for education and research.

Jackman, Shaun D / Mozgacheva, Tatyana / Chen, Susie / O'Huiginn, Brendan / Bailey, Lance / Birol, Inanc / Jones, Steven J M

Bioinformatics (Oxford, England)

2019 Volume 35, Issue 21, Page(s) 4448–4450

Abstract: Summary: The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education ... ...

Abstract	Summary: The ORCA bioinformatics environment is a Docker image that contains hundreds of bioinformatics tools and their dependencies. The ORCA image and accompanying server infrastructure provide a comprehensive bioinformatics environment for education and research. The ORCA environment on a server is implemented using Docker containers, but without requiring users to interact directly with Docker, suitable for novices who may not yet have familiarity with managing containers. ORCA has been used successfully to provide a private bioinformatics environment to external collaborators at a large genome institute, for teaching an undergraduate class on bioinformatics targeted at biologists, and to provide a ready-to-go bioinformatics suite for a hackathon. Using ORCA eliminates time that would be spent debugging software installation issues, so that time may be better spent on education and research. Availability and implementation: The ORCA Docker image is available at https://hub.docker.com/r/bcgsc/orca/. The source code of ORCA is available at https://github.com/bcgsc/orca under the MIT license.
MeSH term(s)	Computational Biology ; Genome ; Software
Language	English
Publishing date	2019-04-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz278
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Article ; Online: Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure.

Jackman, Shaun D / Coombe, Lauren / Warren, René L / Kirk, Heather / Trinh, Eva / MacLeod, Tina / Pleasance, Stephen / Pandoh, Pawan / Zhao, Yongjun / Coope, Robin J / Bousquet, Jean / Bohlmann, Joerg / Jones, Steven J M / Birol, Inanc

Genome biology and evolution

2020 Volume 12, Issue 7, Page(s) 1174–1179

Abstract: Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, ... ...

Abstract	Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads based on sequence homology to the white spruce mitochondrial genome. The assembly graph shows a multipartite genome structure, composed of one smaller 168-kb circular segment of DNA, and a larger 5.4-Mb single component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.
Language	English
Publishing date	2020-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1759-6653
ISSN (online)	1759-6653
DOI	10.1093/gbe/evaa108
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Article ; Online: The western redcedar genome reveals low genetic diversity in a self-compatible conifer.

Shalev, Tal J / Gamal El-Dien, Omnia / Yuen, Macaire M S / Shengqiang, Shu / Jackman, Shaun D / Warren, René L / Coombe, Lauren / van der Merwe, Lise / Stewart, Ada / Boston, Lori B / Plott, Christopher / Jenkins, Jerry / He, Guifen / Yan, Juying / Yan, Mi / Guo, Jie / Breinholt, Jesse W / Neves, Leandro G / Grimwood, Jane /

Rieseberg, Loren H / Schmutz, Jeremy / Birol, Inanc / Kirst, Matias / Yanchuk, Alvin D / Ritland, Carol / Russell, John H / Bohlmann, Joerg

Genome research

2022 Volume 32, Issue 10, Page(s) 1952–1964

Abstract: We assembled the 9.8-Gbp genome of western redcedar (WRC; ...

Abstract	We assembled the 9.8-Gbp genome of western redcedar (WRC;
MeSH term(s)	Tracheophyta/genetics ; Self-Fertilization/genetics ; Alleles ; Heterozygote ; Polymorphism, Genetic ; Genetic Variation ; Selection, Genetic
Language	English
Publishing date	2022-09-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.276358.121
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Zs.A 3729: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

Coombe, Lauren / Zhang, Jessica / Vandervalk, Benjamin P / Chu, Justin / Jackman, Shaun D / Birol, Inanc / Warren, René L

BMC bioinformatics

2018 Volume 19, Issue 1, Page(s) 234

Abstract: Background: The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an ... ...

Abstract	Background: The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time. Results: Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50 = 4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50 = 14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~ 10.5 h compared to 75.7 h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n = 13). Conclusions: ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome datasets. Furthermore, the novel distance estimator in ARKS utilizes barcoding information from linked reads to estimate gap sizes. It accomplishes this by modeling the relationship between known distances of a region within contigs and calculating associated Jaccard indices. ARKS has the potential to provide correct, chromosome-scale genome assemblies, promptly. We expect ARKS to have broad utility in helping refine draft genomes.
MeSH term(s)	Chromosomes, Human/genetics ; Genome, Human ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2018-06-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-018-2243-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada.

Lin, Diana / Coombe, Lauren / Jackman, Shaun D / Gagalova, Kristina K / Warren, René L / Hammond, S Austin / Kirk, Heather / Pandoh, Pawan / Zhao, Yongjun / Moore, Richard A / Mungall, Andrew J / Ritland, Carol / Jaquish, Barry / Isabel, Nathalie / Bousquet, Jean / Jones, Steven J M / Bohlmann, Joerg / Birol, Inanc

Microbiology resource announcements

2019 Volume 8, Issue 23

Abstract: Here, we present the complete chloroplast genome sequence of white spruce ( ...

Abstract	Here, we present the complete chloroplast genome sequence of white spruce (
Language	English
Publishing date	2019-06-06
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00381-19
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sealer: a scalable gap-closing application for finishing draft genomes.

Paulino, Daniel / Warren, René L / Vandervalk, Benjamin P / Raymond, Anthony / Jackman, Shaun D / Birol, Inanç

BMC bioinformatics

2015 Volume 16, Page(s) 230

Abstract: Background: While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low ... ...

Abstract	Background: While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment "gaps" - uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads. Even though there are several tools for closing gaps, they do not easily scale up to processing billion base pair genomes. Results: Here we describe Sealer, a tool designed to close gaps within assembly scaffolds by navigating de Bruijn graphs represented by space-efficient Bloom filter data structures. We demonstrate how it scales to successfully close 50.8% and 13.8% of gaps in human (3 Gbp) and white spruce (20 Gbp) draft assemblies in under 30 and 27 h, respectively - a feat that is not possible with other leading tools with the breadth of data used in our study. Conclusion: Sealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond. Sealer is available for download at https://github.com/bcgsc/abyss/tree/sealer-release.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Genome, Human ; Genome, Plant ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Pinaceae/genetics ; Sequence Analysis, DNA ; User-Computer Interface
Language	English
Publishing date	2015-07-25
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-015-0663-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Assembling genomes using short-read sequencing technology

Jackman, Shaun D / Ä°nanÃ§ Birol

Genome biology. 2010 Jan., v. 11, no. 1

2010

Abstract: Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark. ...

Abstract	Gigabase-scale genome assemblies are now feasible using short-read sequencing technology, bringing the cost of such projects below the million-dollar mark.
Keywords	genome ; genome assembly ; nucleotide sequences
Language	English
Dates of publication	2010-01
Size	p. 2395.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2010-11-1-202
Database	NAL-Catalogue (AGRICOLA)

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