EuPathDB: The Eukaryotic Pathogen database

被引：64

作者：

Aurrecoechea, Cristina ^{[2
]}

Barreto, Ana ^{[1
,3
]}

Brestelli, John ^{[1
,3
]}

Brunk, Brian P. ^{[1
,4
]}

Cade, Shon ^{[1
,4
]}

Doherty, Ryan ^{[1
,4
]}

Fischer, Steve ^{[1
,3
]}

Gajria, Bindu ^{[1
,4
]}

Gao, Xin ^{[1
,4
]}

Gingle, Alan ^{[5
]}

Grant, Greg ^{[1
,3
]}

Harb, Omar S. ^{[1
,4
]}

Heiges, Mark ^{[2
]}

Hu, Sufen ^{[1
,4
]}

Iodice, John ^{[1
,3
]}

Kissinger, Jessica C. ^{[2
,6
,7
]}

Kraemer, Eileen T. ^{[8
]}

Li, Wei ^{[1
,4
]}

Pinney, Deborah F. ^{[1
,3
]}

Pitts, Brian ^{[2
]}

Roos, David S. ^{[4
]}

Srinivasamoorthy, Ganesh ^{[2
]}

Stoeckert, Christian J., Jr. ^{[1
,3
]}

Wang, Haiming ^{[2
]}

Warrenfeltz, Susanne ^{[2
]}

机构：

[1] Univ Penn, Penn Ctr Bioinformat, Philadelphia, PA 19104 USA

[2] Univ Georgia, Ctr Trop & Emerging Global Dis, Athens, GA 30602 USA

[3] Univ Penn, Sch Med, Dept Genet, Philadelphia, PA 19104 USA

[4] Univ Penn, Dept Biol, Philadelphia, PA 19104 USA

[5] Univ Georgia, Plant Genome Mapping Lab, Athens, GA 30602 USA

[6] Univ Georgia, Dept Genet, Athens, GA 30602 USA

[7] Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA

[8] Univ Georgia, Dept Comp Sci, Athens, GA 30602 USA

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / D1期

基金：

英国惠康基金; 美国国家卫生研究院;

关键词：

BIOINFORMATICS RESOURCE; GENOMIC RESOURCES;

D O I：

10.1093/nar/gks1113

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

EuPathDB (http://eupathdb.org) resources include 11 databases supporting eukaryotic pathogen genomic and functional genomic data, isolate data and phylogenomics. EuPathDB resources are built using the same infrastructure and provide a sophisticated search strategy system enabling complex interrogations of underlying data. Recent advances in EuPathDB resources include the design and implementation of a new data loading workflow, a new database supporting Piroplasmida (i.e. Babesia and Theileria), the addition of large amounts of new data and data types and the incorporation of new analysis tools. New data include genome sequences and annotation, strand-specific RNA-seq data, splice junction predictions (based on RNA-seq), phosphoproteomic data, high-throughput phenotyping data, single nucleotide polymorphism data based on high-throughput sequencing (HTS) and expression quantitative trait loci data. New analysis tools enable users to search for DNA motifs and define genes based on their genomic colocation, view results from searches graphically (i.e. genes mapped to chromosomes or isolates displayed on a map) and analyze data from columns in result tables (word cloud and histogram summaries of column content). The manuscript herein describes updates to EuPathDB since the previous report published in NAR in 2010.

引用

页码：D684 / D691

页数：8

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