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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Posted ContentDOI
The worldwide invasion of Drosophila suzukii isaccompanied by a large increase of transposable elementload and a small number of putatively adaptive insertions
V. Merel,Patricia Gibert,I. Buch,V. Rodriguez Rada,Arnaud Estoup,Mathieu Gautier,Marie Fablet,Matthieu Boulesteix,Cristina Vieira +8 more
TL;DR: Using a recently improved genome assembly, the TE content of the spotted wing fly Drosophila suzukii is portrayed and it is found that TEs occupy 47% of the genome and are mostly located in gene poor regions, indicating a recent and probably ongoing TE activity.
Posted ContentDOI
Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing
TL;DR: It is concluded that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics and might warrant more attention by researchers dealing with plant chloroplast genomes.
Journal ArticleDOI
Coding palindromes in mitochondrial genes of Nematomorpha.
Kirill V. Mikhailov,Kirill V. Mikhailov,Boris D. Efeykin,Alexander Y Panchin,Dmitry A. Knorre,Dmitry A. Knorre,Maria D. Logacheva,Maria D. Logacheva,Maria D. Logacheva,Aleksey A. Penin,Aleksey A. Penin,Maria S. Muntyan,Mikhail A. Nikitin,Mikhail A. Nikitin,Olga V. Popova,Olga Zanegina,Mikhail Yu. Vyssokikh,Sergei E. Spiridonov,Vladimir V. Aleoshin,Vladimir V. Aleoshin,Yuri V. Panchin,Yuri V. Panchin +21 more
TL;DR: This work discovered numerous perfect inverted repeats of considerable length embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species, finding that the inverted repeat-containing genes are transcribed and translated into functional proteins.
Journal ArticleDOI
De Novo Transcriptome Characterization of a Sterilizing Trematode Parasite (Microphallus sp.) from Two Species of New Zealand Snails.
Laura Bankers,Maurine Neiman +1 more
TL;DR: In this article, the authors provide transcriptome resources from trematode metacercariae infecting two congeneric snail species, Potamopyrgus antipodarum and P. estuarinus, which are used to produce genomic resources that will be broadly useful to those interested in host-parasite coevolution, local adaptation, and molecular evolution and phylogenetics of this and other snail-trematode systems.
Posted ContentDOI
The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5
Shahid Siddique,Zoran S. Radakovic,C. Hiltl,Clement Pellegrin,Thomas J. Baum,Helen Beasley,O. Chitambo,Divykriti Chopra,Etienne Danchin,Eric Grenier,Samer S. Habash,M. S. Hasan,Johannes Helder,Tarek Hewezi,Julia Holbein,Martijn Holterman,Slawomir Janakowski,Georgios Koutsovoulos,O. P. Kranse,Jose L. Lozano-Torres,Tom R. Maier,Rick E. Masonbrink,Badou Mendy,Esther Riemer,Miroslaw Sobczak,U. Sonawala,Mark G. Sterken,Peter Thorpe,J. J. M. van Steenbrugge,N. Zahid,Florian M. W. Grundler,S. Eves-van den Akker +31 more
TL;DR: In this paper, a dual analysis of host and parasite gene expression over time was performed to identify metabolic pathways that were incomplete in the parasite but complemented by the host, showing that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by horizontal gene transfer from a bacterium, is critically important for parasitism.
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.
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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
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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