Evidence map›Paper›PMID 36781720›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

De Novo Genome Assembly of Japanese Black Cattle as Model of an Economically Relevant Animal.

Shinji Sasaki, Yasuhiko Haga, Hiroyuki Wakaguri, Kazumi Abe, Yutaka Suzuki

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
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.

Shinji SasakiUniversity of the Ryukyus, Faculty of Agriculture, Okinawa, Japan.
Yasuhiko HagaDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Hiroyuki WakaguriDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Kazumi AbeDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
Yutaka SuzukiDepartment of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan. ysuzuki@hgc.jp.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

A genetic analysis of Japanese Black cattle using short reads and guided by the reference genome from Western breeds would miss the structural variation and/or other unique characteristics of Japanese Black cattle. To overcome this difficulty, a de novo genome assembly independent from the reference genome is required. This chapter describes the technical developments, with respect to both experimental and bioinformatics procedures, including the use of short and long reads, required for de novo genome assembly of Japanese Black cattle.

Indexed as

Computational BiologyHigh-Throughput Nucleotide SequencingAnimalsCattleGenomeSequence Analysis, DNADe novo genome assemblyGenetic resourceJapanese Black cattle genome analysisLong-read sequencingNanopore sequencingShort-read sequencing

Identifiers

PMID36781720

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.