Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
| Autor: | Alex N. Salazar, Thomas Abeel |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Statistics and Probability Computer science Population Structural alignment Eccb 2018: European Conference on Computational Biology Proceedings Computational biology Biochemistry Saccharomyces Genome Synteny Structural variation 03 medical and health sciences 0302 clinical medicine education Molecular Biology Gene education.field_of_study Genetic diversity biology Quiver biology.organism_classification Computer Science Applications Computational Mathematics Genome Microbial 030104 developmental biology Computational Theory and Mathematics Microbial genome 030217 neurology & neurosurgery Software Reference genome |
| Zdroj: | Bioinformatics Bioinformatics, 34(17) |
| ISSN: | 1367-4803 |
| DOI: | 10.1093/bioinformatics/bty614 |
| Popis: | Motivation A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world where genome architectures can significantly vary. There is therefore a need for computational methods that can simultaneously analyze the architectures of multiple genomes without introducing bias from a reference. Results In this article, we present Ptolemy: a novel method for studying the diversity of genome architectures - such as structural variation and pan-genomes - across a collection of microbial assemblies without the need of a reference. Ptolemy is a 'top-down' approach to compare whole genome assemblies. Genomes are represented as labeled multi-directed graphs - known as quivers - which are then merged into a single, canonical quiver by identifying 'gene anchors' via synteny analysis. The canonical quiver represents an approximate, structural alignment of all genomes in a given collection encoding structural variation across (sub-) populations within the collection. We highlight various applications of Ptolemy by analyzing structural variation and the pan-genomes of different datasets composing of Mycobacterium, Saccharomyces, Escherichia and Shigella species. Our results show that Ptolemy is flexible and can handle both conserved and highly dynamic genome architectures. Ptolemy is user-friendly - requires only FASTA-formatted assembly along with a corresponding GFF-formatted file - and resource-friendly - can align 24 genomes in ∼10 mins with four CPUs and |
| Databáze: | OpenAIRE |
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