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
A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes
Shan-Shan Zhou,Xue-Mei Yan,Kai-Fu Zhang,Hui Liu,Jie Xu,Shuai Nie,Kai-Hua Jia,Si-Qian Jiao,Wei Zhao,You-Jie Zhao,Ilga Porth,Yousry A. El Kassaby,Tongli Wang,Jian-Feng Mao +13 more
TL;DR: In this article, the authors constructed a plant intact LTR-RTs dataset to classify and annotate intact retrotransposons with a standardized procedure, which currently comprises a total of 2,593,685 intact ltr-rts from genomes of 300 plant species representing 93 families of 46 orders.
Journal ArticleDOI
Taxus yunnanensis genome offers insights into gymnosperm phylogeny and taxol production.
Chi Song,Chi Song,Fang-Fang Fu,Lulu Yang,Yan Niu,Zhaoyang Tian,Xiangxiang He,Yang Xiaoming,Jie Chen,Wei Sun,Tao Wan,Han Zhang,Yicheng Yang,Tian Xiao,Komivi Dossa,Xiangxiao Meng,Fuliang Cao,Yves Van de Peer,Guibin Wang,Shilin Chen +19 more
TL;DR: Song et al. as mentioned in this paper reported a high-quality genome assembly and annotation of Taxus yunnanensis based on 10.7Gb sequences assembled into 12 chromosomes with contig N50 and scaffold N50 of 2.89 and 966.80 Mb, respectively.
Journal ArticleDOI
The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola).
TL;DR: This newly described genome and immune characterization expands the knowledge base for avian genomics and phylogenetics and allows for immune genotyping in the bananaquit, providing tools for the investigation of host-parasite coevolution.
Journal ArticleDOI
Whole-genome assembly and resequencing reveal genomic imprint and key genes of rapid domestication in narrow-leafed lupin
Penghao Wang,Gaofeng Zhou,Gaofeng Zhou,Jianbo Jian,Huaan Yang,Daniel Renshaw,Matthew K Aubert,Jonathan Clements,Tianhua He,M. W. Sweetingham,Chengdao Li,Chengdao Li +11 more
TL;DR: The results identify the key domestication genetic loci and provide the direct genomic evidence for a domestication bottleneck, and open up the possibility of knowledge-driven de novo domestication of wild plants as an avenue to broaden crop plant diversity to enhance food security and sustainable low-carbon emission agriculture.
Journal ArticleDOI
Chromosome restructuring and number change during the evolution of Morus notabilis and Morus alba
TL;DR: It is revealed that long terminal repeat retrotransposons were a major driver of the genome divergence and evolution of the mulberry genomes after they diverged from each other.
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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