Evidence map›Paper›PMID 38077029›Full record

ArticlebioRxiv : the preprint server for biology2023

Interactive visualization of whole eukaryote genome alignments using NCBI's Comparative Genome Viewer (CGV).

Sanjida H Rangwala, Dmitry V Rudnev, Victor V Ananiev, Andrea Asztalos, Barrett Benica, Evgeny A Borodin, Nathan Bouk, Vladislav I Evgeniev, Vamsi K Kodali, Vadim Lotov and 9 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors.

Sanjida H RangwalaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.ORCID 0009-0009-1514-8829
Dmitry V RudnevNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Victor V AnanievNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Andrea AsztalosNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Barrett BenicaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Evgeny A BorodinNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Nathan BoukNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Vladislav I EvgenievNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Vamsi K KodaliNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Vadim LotovNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Eyal MozesNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Dong-Ha OhNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Marina V OmelchenkoNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Sofya SavkinaNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Ekaterina SukharnikovNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Joël VirothaisakunNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Terence D MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Kim D PruittNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.
Valerie A SchneiderNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD 20894, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We report a new visualization tool for analysis of whole genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by NCBI using assembly alignment algorithms developed by us and others. Researchers can examine the alignments between the two assemblies using two alternate views: a chromosome ideogram-based view or a 2D genome dotplot. Whole genome alignment views expose large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed in the ideogram view where available. CGV currently provides approximately 700 alignments from over 300 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization.

Identifiers

PMID38077029
PMCPMC10705539

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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.