Phytozome: a comparative platform for green plant genomics
David Goodstein,Shengqiang Shu,Russell Howson,Rochak Neupane,Richard D. Hayes,Joni Fazo,Therese Mitros,William Dirks,Uffe Hellsten,Nicholas H. Putnam,Daniel S. Rokhsar +10 more
TLDR
Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number of complete plant genomes.Abstract:
The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.read more
Citations
More filters
Journal ArticleDOI
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
David M. Emms,Steven L. Kelly +1 more
TL;DR: A novel orthogroups inference algorithm called OrthoFinder is provided that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy and utility.
Journal ArticleDOI
psRNATarget: a plant small RNA target analysis server
Xinbin Dai,Patrick X. Zhao +1 more
TL;DR: The psRNATarget as mentioned in this paper target analysis server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster.
Journal ArticleDOI
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update.
TL;DR: The updated agriGO that has a largely expanded number of supporting species and datatypes and more visualization features were added to the platform, including SEACOMPARE, direct acyclic graph (DAG) and Scatter Plots, which can be merged by choosing any significant GO term.
Journal ArticleDOI
Sequencing of allotetraploid cotton ( Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Tianzhen Zhang,Yan Hu,Wenkai Jiang,Lei Fang,Xueying Guan,Jiedan Chen,Jinbo Zhang,Christopher A. Saski,Brian E. Scheffler,David M. Stelly,Amanda M. Hulse-Kemp,Qun Wan,Bingliang Liu,Chunxiao Liu,Sen Wang,Mengqiao Pan,Yangkun Wang,Dawei Wang,Wenxue Ye,Lijing Chang,Wenpan Zhang,Qingxin Song,Ryan C. Kirkbride,Xiao-Ya Chen,Elizabeth S. Dennis,Danny J. Llewellyn,Daniel G. Peterson,Peggy Thaxton,Don C. Jones,Qiong Wang,Xiaoyang Xu,Hua Zhang,Huaitong Wu,Lei Zhou,Gaofu Mei,Shuqi Chen,Yue Tian,Dan Xiang,Xinghe Li,Jian Ding,Qiyang Zuo,Linna Tao,Yunchao Liu,Ji Li,Yu Lin,Yuanyuan Hui,Zhisheng Cao,Caiping Cai,Xiefei Zhu,Zhi Jiang,Baoliang Zhou,Wangzhen Guo,Ruiqiang Li,Z. Jeffrey Chen +53 more
TL;DR: Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenomes, suggesting asymmetric evolution.
Journal ArticleDOI
SIFT missense predictions for genomes
TL;DR: The scope of genomic predictions is expanded, with predictions available for more than 200 organisms, and the SIFT 4G algorithm, which is a faster version of SIFT that enables practical computations on reference genomes, is described.
References
More filters
Journal ArticleDOI
MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
KEGG: Kyoto Encyclopedia of Genes and Genomes
Minoru Kanehisa,Susumu Goto +1 more
TL;DR: The Kyoto Encyclopedia of Genes and Genomes (KEGG) as discussed by the authors is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Identification of common molecular subsequences.
TL;DR: This letter extends the heuristic homology algorithm of Needleman & Wunsch (1970) to find a pair of segments, one from each of two long sequences, such that there is no other Pair of segments with greater similarity (homology).