Evidence map›Paper›PMID 24860159›Full record

ArticleBioinformatics (Oxford, England)2014

GenomeVISTA--an integrated software package for whole-genome alignment and visualization.

Alexandre Poliakov, Justin Foong, Michael Brudno, Inna Dubchak

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.

0numbers the graph read from it
0cells of the map it votes in
16citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

16 citing papers in PubMed.

  1. Article
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  4. Article
  5. Article
  6. Review
  7. Article
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  10. Article
  11. Article
  12. Review
  13. Draft genome sequence ofStandards in genomic sciences · 2017
    Article
  14. Article
  15. Review
  16. Ensembl comparative genomics resources.Database : the journal of biological databases and curation · 2016
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Alexandre PoliakovUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
Justin FoongUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
Michael BrudnoUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.
Inna DubchakUS Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA, Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1X8 Canada, Department of Computer Science, University of Toronto, Toronto, ON M5S 3G4 Canada and Genomics Division, LBNL, Berkeley, CA 94720, USA.

Funding

Comparative genomics with the VISTA/LAGAN computational systemR01GM081080 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI DUBCHAK, INNA · 2007 to 2009
$899k
NIGMS NIH HHS R01 GM081080NIGMS NIH HHS R01GM081080A
6 · The paper itself

Abstract

unlabelledWith the ubiquitous generation of complete genome assemblies for a variety of species, efficient tools for whole-genome alignment along with user-friendly visualization are critically important. Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques for comparative analysis. Most of the VISTA programs have been implemented as Web-accessible servers and are extensively used by the biomedical community. In this manuscript, we introduce GenomeVISTA: a novel implementation that incorporates most features of the VISTA family--fast and accurate alignment, visualization capabilities, GUI and analytical tools within a stand-alone software package. GenomeVISTA thus provides flexibility and security for users who need to conduct whole-genome comparisons on their own computers. AVAILABILITY AND IMPLEMENTATION: Implemented in Perl, C/C++ and Java, the source code is freely available for download at the VISTA Web site: http://genome.lbl.gov/vista/.

Indexed as

SoftwareAlgorithmsComputer GraphicsGenomicsSequence Alignment

Identifiers

PMID24860159
PMCPMC4155257

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.