Evidence map›Paper›PMID 38798552›Full record

ArticlebioRxiv : the preprint server for biology2024

Combining DNA and protein alignments to improve genome annotation with LiftOn.

Kuan-Hao Chao, Jakob M Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, Steven L Salzberg

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

7 authors.

Kuan-Hao ChaoDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-0099-0692
Jakob M HeinzDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0002-9218-2643
Celine HohDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0009-0001-6896-125X
Alan MaoDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-2381-0607
Alaina ShumateCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
Mihaela PerteaDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0003-0762-8637
Steven L SalzbergDepartment of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA.ORCID 0000-0002-8859-7432

Funding

Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8M
Computational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7M
Computational Methods for Microbial and Microbiome Sequence AnalysisR35GM130151 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Steven L. Salzberg · 2019 to 2026
$2.9M
NHGRI NIH HHS R01 HG006677NHGRI NIH HHS T32 HG002295NIGMS NIH HHS R35 GM130151
6 · The paper itself

Abstract

As the number and variety of assembled genomes continues to grow, the number of annotated genomes is falling behind, particularly for eukaryotes. DNA-based mapping tools help to address this challenge, but they are only able to transfer annotation between closely-related species. Here we introduce LiftOn, a homology-based software tool that integrates DNA and protein alignments to enhance the accuracy of genome-scale annotation and to allow mapping between relatively distant species. LiftOn's protein-centric algorithm considers both types of alignments, chooses optimal open reading frames, resolves overlapping gene loci, and finds additional gene copies where they exist. LiftOn can reliably transfer annotation between genomes representing members of the same species, as we demonstrate on human, mouse, honey bee, rice, and

Identifiers

PMID38798552
PMCPMC11118573

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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.