Evidence map›Paper›PMID 23956303›Full record

ArticleBioinformatics (Oxford, England)2013

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

Darren S Curtis, Aaron R Phillips, Stephen J Callister, Sean Conlan, Lee Ann McCue

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Itaconic acid production is regulated by LaeA inMetabolic engineering communications · 2022
    Article
  2. Article
  3. Complete genome sequence ofBiotechnology reports (Amsterdam, Netherlands) · 2019
    Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. 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

5 authors.

Darren S CurtisComputational & Statistical Analytics Division, Pacific Northwest National Laboratory, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA, Genetics and Molecular Biology Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA and Computational Sciences & Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
Aaron R Phillips
Stephen J Callister
Sean Conlan
Lee Ann McCue

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

summaryAt the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

Indexed as

GenomeGenomicsInternetProgramming LanguagesProteinsSoftware DesignProteins

Identifiers

PMID23956303
PMCPMC3841380

What OpenQuestion holds

Textmetadata
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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.