Paper Info
Title
Companion: a web server for annotation and analysis of parasite genomes.
Abstract
Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion.sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.
Year
DOI
Venue
2016
10.1093/nar/gkw292
NUCLEIC ACIDS RESEARCH
Field
DocType
Volume
Pseudogene,Genome,Annotation,Biology,Genome project,Gene prediction,Genetics,Sequence assembly,Vertebrate and Genome Annotation Project,Web server
Journal
44
Issue
ISSN
Citations 
W1
0305-1048
0
PageRank 
References 
Authors
0.34
17
7
Name
Order
Citations
PageRank
Sascha Steinbiss1434.43
Fatima Silva-Franco250.77
B. P. Brunk333742.80
Bernardo Foth400.34
Christiane Hertz-Fowler5968.46
Matthew Berriman600.34
Thomas D Otto71016.89