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
Refined ab initio gene predictions of Heterorhabditis bacteriophora using RNA-seq.
Jonathan Vadnal,Olivia G. Granger,Ramesh Ratnappan,Ioannis Eleftherianos,Damien M. O'Halloran,John M. Hawdon +5 more
TL;DR: A methodology is presented for leveraging RNA-seq evidence to generate improved annotations using ab initio gene prediction software for entomopathogenic nematode Heterorhabditis bacteriophora, demonstrating the importance of coupling transcriptional data with genome assemblies.
Posted ContentDOI
Seqping: Gene Prediction Pipeline for Plant Genomes using Self- Trained Gene Models and Transcriptomic Data
Kuang-Lim Chan,Rozana Rosli,Tatiana V. Tatarinova,Michael Hogan,Mohd Firdaus-Raih,Eng-Ti Leslie Low +5 more
TL;DR: An automated pipeline that performs gene prediction using selftrained HMM models and transcriptomic data is reported that performed better than the use of the closest related HMM from a standalone program.
Dissertation
Developing a bioinformatics framework for proteogenomics
TL;DR: It is critically important to incorporate proteomics data into genome annotation pipelines to provide experimental protein-coding evidence, and this thesis addresses the existing gap between the use of genomic and proteomic sources for accurate genome annotation by applying a proteogenomics approach with a customised methodology.
Journal ArticleDOI
Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes.
Kristina Gagalova,René L. Warren,Lauren Coombe,Johnathan Wong,Ka Ming Nip,Macaire M.S. Yuen,Justin G. A. Whitehill,Jose M. Celedon,Carol Ritland,Greg Taylor,Dean Cheng,Patrick Plettner,S. Austin Hammond,Hamid Mohamadi,Yongjun Zhao,Richard A. Moore,Andrew J. Mungall,Brian Boyle,Jérôme Laroche,Joan Cottrell,John MacKay,Manuel Lamothe,Sébastien Gérardi,Nathalie Isabel,Nathalie Pavy,Steven J.M. Jones,Joerg Bohlmann,Jean Bousquet,Inanc Birol +28 more
TL;DR: Improved and more contiguous spruce giga-genome sequences should strengthen the understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level.
Posted ContentDOI
Long Read Annotation (LoReAn): automated eukaryotic genome annotation based on long-read cDNA sequencing
David Cook,Jose Espejo Valle-Inclan,Alice Pajoro,Hanna Rovenich,Bart P. H. J. Thomma,Luigi Faino +5 more
TL;DR: It is shown that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA sequencing data generated from either the PacBio or MinION sequencing platforms, and correctly predicting gene structure and capturing genes missed by other annotation pipelines.
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.
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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
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