Kollmar, Martin

[["dc.bibliographiccitation.firstpage","422"],["dc.bibliographiccitation.journal","BMC genomics"],["dc.bibliographiccitation.lastpage","422"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Pillmann, Holger"],["dc.contributor.author","Keller, Oliver"],["dc.contributor.author","Waack, Stephan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-09T11:40:39Z"],["dc.date.available","2019-07-09T11:40:39Z"],["dc.date.issued","2008"],["dc.description.abstract","BACKGROUND: Obtaining the gene structure for a given protein encoding gene is an important step in many analyses. A software suited for this task should be readily accessible, accurate, easy to handle and should provide the user with a coherent representation of the most probable gene structure. It should be rigorous enough to optimise features on the level of single bases and at the same time flexible enough to allow for cross-species searches. RESULTS: WebScipio, a web interface to the Scipio software, allows a user to obtain the corresponding coding sequence structure of a here given a query protein sequence that belongs to an already assembled eukaryotic genome. The resulting gene structure is presented in various human readable formats like a schematic representation, and a detailed alignment of the query and the target sequence highlighting any discrepancies. WebScipio can also be used to identify and characterise the gene structures of homologs in related organisms. In addition, it offers a web service for integration with other programs. CONCLUSION: WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query. It offers more than 250 eukaryotic genomes that can be searched and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike. WebScipio is freely accessible at http://www.webscipio.org."],["dc.identifier.doi","10.1186/1471-2164-9-422"],["dc.identifier.pmid","18801164"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11177"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/58223"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1471-2164"],["dc.rights","CC BY 2.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.0/"],["dc.subject.mesh","Algorithms"],["dc.subject.mesh","Amino Acid Sequence"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Databases, Genetic"],["dc.subject.mesh","Genomics"],["dc.subject.mesh","Humans"],["dc.subject.mesh","Sequence Alignment"],["dc.subject.mesh","Sequence Analysis, DNA"],["dc.subject.mesh","Sequence Analysis, Protein"],["dc.subject.mesh","Software"],["dc.subject.mesh","Species Specificity"],["dc.subject.mesh","User-Computer Interface"],["dc.title","WebScipio: an online tool for the determination of gene structures using protein sequences."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","47"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC genomics"],["dc.bibliographiccitation.lastpage","47"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Glöckner, Gernot"],["dc.date.accessioned","2019-07-09T11:54:23Z"],["dc.date.available","2019-07-09T11:54:23Z"],["dc.date.issued","2003-11-27"],["dc.description.abstract","BACKGROUND: Kinesins constitute a large superfamily of motor proteins in eukaryotic cells. They perform diverse tasks such as vesicle and organelle transport and chromosomal segregation in a microtubule- and ATP-dependent manner. In recent years, the genomes of a number of eukaryotic organisms have been completely sequenced. Subsequent studies revealed and classified the full set of members of the kinesin superfamily expressed by these organisms. For Dictyostelium discoideum, only five kinesin superfamily proteins (Kif's) have already been reported. RESULTS: Here, we report the identification of thirteen kinesin genes exploiting the information from the raw shotgun reads of the Dictyostelium discoideum genome project. A phylogenetic tree of 390 kinesin motor domain sequences was built, grouping the Dictyostelium kinesins into nine subfamilies. According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass. CONCLUSION: This analysis of the Dictyostelium genome led to the identification of eight new kinesin motor proteins. According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis. Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions."],["dc.identifier.doi","10.1186/1471-2164-4-47"],["dc.identifier.pmid","14641909"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60649"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1471-2164"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.mesh","Animals"],["dc.subject.mesh","Dictyostelium"],["dc.subject.mesh","Kinesin"],["dc.subject.mesh","Molecular Motor Proteins"],["dc.subject.mesh","Phylogeny"],["dc.subject.mesh","Protozoan Proteins"],["dc.subject.mesh","Terminology as Topic"],["dc.title","Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]