Journal ArticleDOI
GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
TLDR
The GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs, strictly follow the annotation graph approach, offering a unified graph-based representation.Abstract:
Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface.read more
Citations
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Journal ArticleDOI
Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase.
Domenico Giosa,Maria Rosa Felice,Letterio Giuffrè,Riccardo Aiese Cigliano,Andreu Paytuví-Gallart,Carla Lo Passo,Cinzia Barresi,Enrico D'Alessandro,Huaiqiu Huang,Giuseppe Criseo,Héctor M. Mora-Montes,Sybren de Hoog,Orazio Romeo +12 more
TL;DR: The global transcriptomic differences occurring between mould and yeast phases of S. schenckii are reported, including changes in gene expression profiles associated with these distinct cellular phenotypes, and a new genome annotation is proposed, which reveals a more complex transcriptional architecture than previously assumed.
Journal ArticleDOI
Genomic distribution of a novel Pyrenophora tritici-repentis ToxA insertion element.
TL;DR: A novel 166 bp insertion element (PtrHp1) which can form a perfectly matched 59 bp inverted repeat hairpin structure located downstream of the ToxA coding sequence in the 3' UTR exon is uncovered and may contribute towards future understanding of the possible role of hairpin elements in Ptr.
Journal ArticleDOI
Genetic Identification of Species Responsible for Depredation in Commercial and Recreational Fisheries
J. Marcus Drymon,Pearce T. Cooper,Sean P. Powers,Molly M. Miller,Sharon F. Magnuson,Evan Krell,Christopher E. Bird +6 more
TL;DR: The findings provide a basis for the development of a genetic technique for predator identification, while highlighting challenges to be overcome before predator identification can be applied to large‐scale fisheries.
Posted ContentDOI
SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica
TL;DR: The availability of the chromosome-length genome assembly of M. indica will provide novel insights into genome evolution, understand the genetic basis of specialized phytochemical composites relevant to fruit quality, and enhance allele mining in genomics-assisted breeding for mango genetic improvement.
Journal ArticleDOI
The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies
TL;DR: Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively.
References
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BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
Journal ArticleDOI
The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
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