publication . Article . 2016

Companion: a web server for annotation and analysis of parasite genomes

Steinbiss, Sascha; Silva-Franco, Fatima; Brunk, Brian; Foth, Bernardo; Hertz-Fowler, Christiane; Berriman, Matthew; Otto, Thomas D.;
Open Access English
  • Published: 08 Jul 2016 Journal: Nucleic Acids Research, volume 44, issue Web Server issue, pages W29-W34 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press
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...
Subjects
free text keywords: Web Server issue
Funded by
WT| Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098051
  • Funding stream: Cellular and Molecular Neuroscience ; Molecules, Genes and Cells
,
WT| Integrated bioinformatics resources for kinetoplastid pathogens.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 099198
  • Funding stream: Immunology and Infectious Disease ; Immune System in Health and Disease
39 references, page 1 of 3

Foth, B.J., Otto, T.D.. Genomics illuminates parasite biology. Nat. Rev. Microbiol.. 2014; 12: 727 [PubMed]

Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T.. Gene ontology: tool for the unification of biology. Nat. Genet.. 2000; 25: 25-29 [OpenAIRE] [PubMed]

Gene Ontology Consortium: going forward. Nucleic Acids Res.. 2014; 43: D1049-D1056 [OpenAIRE] [PubMed]

Seemann, T.. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30: 2068-2069 [PubMed]

Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M.. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9: 75 [OpenAIRE] [PubMed]

Cantarel, B.L., Korf, I., Robb, S. M.C., Parra, G., Ross, E., Moore, B., Holt, C., Sánchez Alvarado, A., Yandell, M.. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res.. 2008; 18: 188-196 [OpenAIRE] [PubMed]

Holt, C., Yandell, M.. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinform. 2011; 12: 491

Stanke, M., Schöffmann, O., Morgenstern, B., Waack, S.. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinform.. 2006; 7: 62 [OpenAIRE]

Korf, I.. Gene finding in novel genomes. BMC Bioinform.. 2004; 5: 59 [OpenAIRE]

Li, L., Stoeckert, C.J., Roos, D.S.. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res.. 2003; 13: 2178-2189 [OpenAIRE] [PubMed]

Pirovano, W., Boetzer, M., Derks, M.F.L., Smit, S.. NCBI-compliant genome submissions: tips and tricks to save time and money: Table 1. Brief. Bioinform.. 2015; 2015: bbv104 [PubMed]

Otto, T.D., Dillon, G.P., Degrave, W.S., Berriman, M.. RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res.. 2011; 39: e57 [OpenAIRE] [PubMed]

Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S.E., Behr, J., Bertone, P.. Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods. 2013; 10: 1177-1184 [OpenAIRE] [PubMed]

Lomsadze, A., Burns, P.D., Borodovsky, M.. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Res.. 2014; 42: e119 [OpenAIRE] [PubMed]

Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Heger, A., Hetherington, K., Holm, L., Mistry, J.. Pfam: the protein families database. Nucleic Acids Res.. 2014; 42: D222-D230 [OpenAIRE] [PubMed]

39 references, page 1 of 3
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...
Subjects
free text keywords: Web Server issue
Funded by
WT| Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 098051
  • Funding stream: Cellular and Molecular Neuroscience ; Molecules, Genes and Cells
,
WT| Integrated bioinformatics resources for kinetoplastid pathogens.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 099198
  • Funding stream: Immunology and Infectious Disease ; Immune System in Health and Disease
39 references, page 1 of 3

Foth, B.J., Otto, T.D.. Genomics illuminates parasite biology. Nat. Rev. Microbiol.. 2014; 12: 727 [PubMed]

Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T.. Gene ontology: tool for the unification of biology. Nat. Genet.. 2000; 25: 25-29 [OpenAIRE] [PubMed]

Gene Ontology Consortium: going forward. Nucleic Acids Res.. 2014; 43: D1049-D1056 [OpenAIRE] [PubMed]

Seemann, T.. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014; 30: 2068-2069 [PubMed]

Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., Disz, T., Edwards, R.A., Formsma, K., Gerdes, S., Glass, E.M.. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008; 9: 75 [OpenAIRE] [PubMed]

Cantarel, B.L., Korf, I., Robb, S. M.C., Parra, G., Ross, E., Moore, B., Holt, C., Sánchez Alvarado, A., Yandell, M.. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res.. 2008; 18: 188-196 [OpenAIRE] [PubMed]

Holt, C., Yandell, M.. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinform. 2011; 12: 491

Stanke, M., Schöffmann, O., Morgenstern, B., Waack, S.. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinform.. 2006; 7: 62 [OpenAIRE]

Korf, I.. Gene finding in novel genomes. BMC Bioinform.. 2004; 5: 59 [OpenAIRE]

Li, L., Stoeckert, C.J., Roos, D.S.. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res.. 2003; 13: 2178-2189 [OpenAIRE] [PubMed]

Pirovano, W., Boetzer, M., Derks, M.F.L., Smit, S.. NCBI-compliant genome submissions: tips and tricks to save time and money: Table 1. Brief. Bioinform.. 2015; 2015: bbv104 [PubMed]

Otto, T.D., Dillon, G.P., Degrave, W.S., Berriman, M.. RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res.. 2011; 39: e57 [OpenAIRE] [PubMed]

Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S.E., Behr, J., Bertone, P.. Assessment of transcript reconstruction methods for RNA-seq. Nat. Methods. 2013; 10: 1177-1184 [OpenAIRE] [PubMed]

Lomsadze, A., Burns, P.D., Borodovsky, M.. Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm. Nucleic Acids Res.. 2014; 42: e119 [OpenAIRE] [PubMed]

Finn, R.D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Heger, A., Hetherington, K., Holm, L., Mistry, J.. Pfam: the protein families database. Nucleic Acids Res.. 2014; 42: D222-D230 [OpenAIRE] [PubMed]

39 references, page 1 of 3
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publication . Article . 2016

Companion: a web server for annotation and analysis of parasite genomes

Steinbiss, Sascha; Silva-Franco, Fatima; Brunk, Brian; Foth, Bernardo; Hertz-Fowler, Christiane; Berriman, Matthew; Otto, Thomas D.;