Family-Free Genome Comparison.

Marilia D V Braga, Daniel Doerr, Diego P Rubert, Jens Stoye

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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.

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2 · The registry

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

4 authors.

Marilia D V BragaFaculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.

Daniel DoerrDepartment for Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, German Diabetes Center (DDZ), Leibniz Institute for Diabetes Research, and Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany.

Diego P RubertFaculdade de Computacão, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil.

Jens StoyeFaculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany. jens.stoye@uni-bielefeld.de.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The comparison of large-scale genome structures across distinct species offers valuable insights into the species' phylogeny, genome organization, and gene associations. In this chapter, we review the family-free genome comparison tool FFGC that, relying on built-in interfaces with a sequence comparison tool (either BLAST+ or DIAMOND) and with an ILP solver (either CPLEX or Gurobi), provides several methods for analyses that do not require prior classification of genes across the studied genomes. Taking annotated genome sequences as input, FFGC is a complete workflow for genome comparison allowing not only the computation of measures of similarity and dissimilarity but also the inference of gene families, simultaneously based on sequence similarities and large-scale genomic features.

Indexed as

GenomicsPhylogenySoftwareComputational BiologyGenomeHumansCommon intervalsConserved adjacenciesDouble-cut-and-joinGene family-freeGene order analysisGene orthology inferenceGenome distanceGenome medianGenome similarity

Identifiers

PMID38819556

DOI10.1186/1471-2105-12-124

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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.