Evidence map›Paper›PMID 19461980›Full record

ArticleEvolutionary bioinformatics online2007

Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis.

Holly A Basta, Alex J Buzak, Marcella A McClure

Abstract read
PubMed Full text at PMC
In one paragraph

Article in Evolutionary bioinformatics online, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Article
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  6. Review
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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

3 authors.

Holly A BastaDepartment of Microbiology and the Center for Computational Biology, Montana State University at Bozeman, 109 Lewis Hall, Bozeman, MT 59717, U.S.A.
Alex J Buzak
Marcella A McClure

Funding

MT INBRE RESEARCH COREP20RR016455 · NCRR · MONTANA STATE UNIVERSITY - BOZEMAN · PI HARMSEN, ALLEN G · 2001 to 2011
$34.4M
COMPUTER-BASED SEQUENCE ANALYSIS AND RNA VIRUS EVOLUTIONR01AI028309 · NIAID · UNIVERSITY OF NEVADA LAS VEGAS · PI MCCLURE, MARCELLA A · 1990 to 2007
$1.2M
NCRR NIH HHS P20 RR016455NIAID NIH HHS R01 AI028309
6 · The paper itself

Abstract

Retroid agents are genomes that encode a reverse transcriptase (RT) and replicate or transpose by way of an RNA intermediate. The Genome Parsing Suite (GPS) is software created to identify and characterize Retroid agents in any genome database (McClure et al. 2005). The detailed analysis of all Retroid agents found by the GPS in Danio rerio (zebrafish), Oryzias latipes (medaka), Gasterosteus aculeatus (stickleback) and Tetraodon nigroviridis (spotted green pufferfish) reveals extensive Retroid agent diversity in the compact genomes of all four fish. Novel Retroid agents were identified by the GPS software: the telomerase reverse transcriptase (TERT) in O. latipes, G. aculeatus and T. nigroviridis and a potential TERT in D. rerio, a retrotransposon in D. rerio, and multiple lineages of endogenous retroviruses (ERVs) in D. rerio, O. latipes and G. aculeatus.

Indexed as

Danio rerioGasterosteus aculeatusGenome Parsing Suite softwareOryzias latipesRetroidTetraodon nigroviridistransposable elements

Identifiers

PMID19461980
PMCPMC2684134

What OpenQuestion holds

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Registered trials

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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.