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
An improved assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family
TL;DR: A chromosome-level assembly of the hop genome was performed in this paper , using a controlled bi-parental mapping population to identify significant sex-associated markers from the mapping population.
Posted ContentDOI
Haplotype-resolved assembly of the African catfish (Clarias gariepinus) provides insights for semi-terrestrial adaptation of airbreathing catfishes
TL;DR: In this paper , the authors sequenced the genome of the African catfish Clarias gariepinus, one of the most commonly farmed clariids, and generated a chromosome-level assembly with high-resolution haplotypes, including the male-specific haplotype.
Posted ContentDOI
Genome assembly of the polyclad flatworm <i>Prostheceraeus crozieri</i>
Serkan Unal,Aarón Zau NKosi Rio +1 more
TL;DR: Prostheceraeus crozieri as mentioned in this paper is an emerging model polyclad flatworm that already has some useful transcriptome data but, to date, no sequenced genome.
Proceedings ArticleDOI
Agent Technology for Data Analytics of Gene Expression Data: A Literature Review
K Santhosh,S Ajitha +1 more
TL;DR: This research paper gives an overall function of multi agent systems in analytics of gene expression data, in terms of characteristics, adaptability, reliability and robotics of agents.
Posted ContentDOI
Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions
TL;DR: SeqOutBias as discussed by the authors was developed to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymes' sequence biases, which can interfere with the accurate interpretation of these data.
References
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TL;DR: The book is an introduction to the idea of design patterns in software engineering, and a catalog of twenty-three common patterns, which most experienced OOP designers will find out they've known about patterns all along.
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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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