Companion: a web server for annotation and analysis of parasite genomes.
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.
Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK ss34@sanger.ac.uk.
Sascha
0000-0002-2151-0574
S
Steinbiss
Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
Fatima
F
Silva-Franco
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
Brian
B
Brunk
Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
Bernardo
B
Foth
Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
Christiane
C
Hertz-Fowler
Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
Matthew
M
Berriman
Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
Thomas D
TD
Otto
D030541:Databases, Genetic; D063990:Gene Ontology; D018503:Genome, Protozoan; D020407:Internet; D007891:Leishmania / Q000145:classification / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D010963:Plasmodium falciparum / Q000145:classification / Q000235:genetics*; D015800:Protozoan Proteins / Q000235:genetics*; D016053:RNA, Protozoan / Q000235:genetics*; D012680:Sensitivity and Specificity; D012984:Software
D015800:Protozoan Proteins; D016053:RNA, Protozoan