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
More filters
Journal ArticleDOI
Genomic re-assessment of the transposable element landscape of the potato genome.
Diego Zavallo,Juan Manuel Crescente,Juan Manuel Crescente,Magdalena Gantuz,Melisa Leone,Leonardo Sebastián Vanzetti,Leonardo Sebastián Vanzetti,Ricardo Williams Masuelli,Sebastian Asurmendi +8 more
TL;DR: A comprehensive and reliable potato TE landscape is provided, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community.
Posted ContentDOI
Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia
R. van Velzen,Rens Holmer,Fengjiao Bu,L.J.J. Rutten,A.L. van Zeijl,Liu W,Luca Santuari,Qingqin Cao,Trupti Sharma,Defeng Shen,Yuda Purwana Roswanjaya,Titis A. K. Wardhani,M. Seifi Kalhor,Joelle Jansen,D.J. van den Hoogen,Berivan Gungor,Marijke Hartog,J. Hontelez,J.W.G. Verver,Wei-Cai Yang,Elio Schijlen,Rimi Repin,Menno Schilthuizen,M.E. Schranz,Renze Heidstra,Kana Miyata,Elena Fedorova,Wouter Kohlen,A.H.J. Bisseling,Sandra Smit,René Geurts +30 more
TL;DR: Comparing genomes of Parasponia and its non-nodulating relative Trema did not reveal specific gene duplications that could explain a recent gain of nodulation, but showed evidence of pseudogenization or loss of key symbiosis genes, demonstrating that these species have lost the potential to nodulate.
Journal ArticleDOI
Genomics as a service: A joint computing and networking perspective
TL;DR: It emerges that virtualization, both in computing and networking, is the key for a successful large-scale exploitation of genomic data, by pushing ahead the adoption of the GaaS paradigm.
Journal ArticleDOI
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
Matej Lexa,Matej Lexa,Pavel Jedlička,Ivan Vanat,Michal Cervenansky,Michal Cervenansky,Eduard Kejnovsky +6 more
TL;DR: This work created software that uses a greedy recursive algorithm to mine increasingly fragmented copies of full-length LTR retrotransposons in assembled genomes and other sequence data and found TE-greedy-nester to be superior in a number of parameters, namely computation time and full- length TE recovery in highly nested regions.
Journal ArticleDOI
Epigenetic silencing of V(D)J recombination is a major determinant for selective differentiation of mucosal-associated invariant t cells from induced pluripotent stem cells
TL;DR: The methylome and transcriptome analyses of MAITs during the course of differentiation from iPSCs revealed that recombination-activating genes (RAG1 and RAG2) and DNA nucleotidylexotransferase (DNTT) were highly methylated with their expression being repressed throughout differentiation.
References
More filters
Book
Design Patterns: Elements of Reusable Object-Oriented Software
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.
Book
Introduction to Algorithms
TL;DR: The updated new edition of the classic Introduction to Algorithms is intended primarily for use in undergraduate or graduate courses in algorithms or data structures and presents a rich variety of algorithms and covers them in considerable depth while making their design and analysis accessible to all levels of readers.
Journal ArticleDOI
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.
Book ChapterDOI
Introduction to Algorithms
TL;DR: This chapter provides an overview of the fundamentals of algorithms and their links to self-organization, exploration, and exploitation.
Related Papers (5)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more