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
The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis.
Lisong Hu,Zhongping Xu,Maojun Wang,Rui Fan,Daojun Yuan,Baoduo Wu,Huasong Wu,Xiaowei Qin,Lin Yan,Lehe Tan,Soonliang Sim,Wen Li,Christopher A. Saski,Henry Daniell,Jonathan F. Wendel,Keith Lindsey,Xianlong Zhang,Chaoyun Hao,Shuangxia Jin +18 more
TL;DR: The authors assemble the reference genome of this species and analyze gene families associated with piperine biosynthesis and shed light on the metabolic processes relevant to the molecular basis of species-specific piperin biosynthesis.
Journal ArticleDOI
Companion: a web server for annotation and analysis of parasite genomes
Sascha Steinbiss,Fatima Silva-Franco,Brian P. Brunk,Bernardo J. Foth,Christiane Hertz-Fowler,Matthew Berriman,Thomas D. Otto +6 more
TL;DR: The Companion web server is developed providing parasite genome annotation as a service using a reference-based approach and the use and performance is demonstrated by annotating two Leishmania and Plasmodium genomes as typical parasite cases and compared to manually annotated references.
Journal ArticleDOI
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom.
Swaraj Basu,Shrikant Patil,Daniel Mapleson,Monia Teresa Russo,Laura Vitale,Cristina Fevola,Florian Maumus,Raffaella Casotti,Thomas Mock,Mario Caccamo,Marina Montresor,Remo Sanges,Maria Immacolata Ferrante +12 more
TL;DR: The controllable life cycle and genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence
Sebastian Eves-van den Akker,Dominik R. Laetsch,Peter Thorpe,Catherine J. Lilley,Etienne Danchin,Rocha, Da, Martine,Corinne Rancurel,Nancy Holroyd,James Cotton,Amir Szitenberg,Eric Grenier,Josselin Montarry,Benjamin Mimee,Marc Olivier Duceppe,Ian Boyes,Jessica Marvin,Laura M. Jones,Hazijah Yusup,Joël Lafond-Lapalme,Magali Esquibet,Michael Sabeh,Michael Rott,Hein Overmars,A.M. Finkers-Tomczak,Geert Smant +24 more
TL;DR: For each gene, the authors lists the normalized expression data for each life stage, and (if significantly differentially expressed) which expression super cluster it is grouped into, for each gene.
Journal ArticleDOI
Recompleting the Caenorhabditis elegans genome.
Jun Yoshimura,Kazuki Ichikawa,Massa J. Shoura,Karen L. Artiles,Idan Gabdank,Lamia Wahba,Cheryl L. Smith,Mark L. Edgley,Ann E. Rougvie,Andrew Fire,Shinichi Morishita,Erich M. Schwarz +11 more
TL;DR: This long-read assembly of VC2010, a modern strain derived from N2, has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications, and predicted ≥53 new genes in VC2010.
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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