Kollmar, Martin

[["dc.bibliographiccitation.firstpage","103"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Hellkamp, Marcel"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2021-06-01T10:47:58Z"],["dc.date.available","2021-06-01T10:47:58Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1186/1471-2164-8-103"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85785"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.issn","1471-2164"],["dc.title","diArk – a resource for eukaryotic genome research"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","173"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Becker, Sebastian"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-09T11:52:53Z"],["dc.date.available","2019-07-09T11:52:53Z"],["dc.date.issued","2009"],["dc.description.abstract","Background: Motor proteins have extensively been studied in the past and consist of large superfamilies. They are involved in diverse processes like cell division, cellular transport, neuronal transport processes, or muscle contraction, to name a few. Vertebrates contain up to 60 myosins and about the same number of kinesins that are spread over more than a dozen distinct classes. Results: Here, we present the comparative genomic analysis of the motor protein repertoire of 21 completely sequenced arthropod species using the owl limpet Lottia gigantea as outgroup. Arthropods contain up to 17 myosins grouped into 13 classes. The myosins are in almost all cases clear paralogs, and thus the evolution of the arthropod myosin inventory is mainly determined by gene losses. Arthropod species contain up to 29 kinesins spread over 13 classes. In contrast to the myosins, the evolution of the arthropod kinesin inventory is not only determined by gene losses but also by many subtaxon-specific and species-specific gene duplications. All arthropods contain each of the subunits of the cytoplasmic dynein/dynactin complex. Except for the dynein light chains and the p150 dynactin subunit they contain single gene copies of the other subunits. Especially the roadblock light chain repertoire is very species-specific. Conclusion: All 21 completely sequenced arthropods, including the twelve sequenced Drosophila species, contain a species-specific set of motor proteins. The phylogenetic analysis of all genes as well as the protein repertoire placed Daphnia pulex closest to the root of the Arthropoda. The louse Pediculus humanus corporis is the closest relative to Daphnia followed by the group of the honeybee Apis mellifera and the jewel wasp Nasonia vitripennis. After this group the rust-red flour beetle Tribolium castaneum and the silkworm Bombyx mori diverged very closely from the lineage leading to the Drosophila species."],["dc.identifier.doi","10.1186/1471-2164-10-173"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/6141"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60300"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","540"],["dc.title","Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","300"],["dc.bibliographiccitation.firstpage","300-1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.lastpage","300-8"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-09T11:54:22Z"],["dc.date.available","2019-07-09T11:54:22Z"],["dc.date.issued","2006"],["dc.description.abstract","Background: Annotation of protein sequences of eukaryotic organisms is crucial for the understanding of their function in the cell. Manual annotation is still by far the most accurate way to correctly predict genes. The classification of protein sequences, their phylogenetic relation and the assignment of function involves information from various sources. This often leads to a collection of heterogeneous data, which is hard to track. Cytoskeletal and motor proteins consist of large and diverse superfamilies comprising up to several dozen members per organism. Up to date there is no integrated tool available to assist in the manual large-scale comparative genomic analysis of protein families. Description: Pfarao (Protein Family Application for Retrieval, Analysis and Organisation) is a database driven online working environment for the analysis of manually annotated protein sequences and their relationship. Currently, the system can store and interrelate a wide range of information about protein sequences, species, phylogenetic relations and sequencing projects as well as links to literature and domain predictions. Sequences can be imported from multiple sequence alignments that are generated during the annotation process. A web interface allows to conveniently browse the database and to compile tabular and graphical summaries of its content. Conclusion: We implemented a protein sequence-centric web application to store, organize, interrelate, and present heterogeneous data that is generated in manual genome annotation and comparative genomics. The application has been developed for the analysis of cytoskeletal and motor proteins (CyMoBase) but can easily be adapted for any protein."],["dc.identifier.doi","10.1186/1471-2164-7-300"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60644"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Pfarao: a web application for protein family analysis customized for cytoskeletal and motor proteins (CyMoBase)"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","R196"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Genome Biology"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2021-06-01T10:48:01Z"],["dc.date.available","2021-06-01T10:48:01Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1186/gb-2007-8-9-r196"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85804"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.issn","1465-6906"],["dc.title","Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["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.artnumber","77"],["dc.bibliographiccitation.journal","BMC Bioinformatics"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Waack, Stephan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-07T09:27:09Z"],["dc.date.available","2018-11-07T09:27:09Z"],["dc.date.issued","2013"],["dc.description.abstract","Background: All sequenced eukaryotic genomes have been shown to possess at least a few introns. This includes those unicellular organisms, which were previously suspected to be intron-less. Therefore, gene splicing must have been present at least in the last common ancestor of the eukaryotes. To explain the evolution of introns, basically two mutually exclusive concepts have been developed. The introns-early hypothesis says that already the very first protein-coding genes contained introns while the introns-late concept asserts that eukaryotic genes gained introns only after the emergence of the eukaryotic lineage. A very important aspect in this respect is the conservation of intron positions within homologous genes of different taxa. Results: GenePainter is a standalone application for mapping gene structure information onto protein multiple sequence alignments. Based on the multiple sequence alignments the gene structures are aligned down to single nucleotides. GenePainter accounts for variable lengths in exons and introns, respects split codons at intron junctions and is able to handle sequencing and assembly errors, which are possible reasons for frame-shifts in exons and gaps in genome assemblies. Thus, even gene structures of considerably divergent proteins can properly be compared, as it is needed in phylogenetic analyses. Conserved intron positions can also be mapped to user-provided protein structures. For their visualization GenePainter provides scripts for the molecular graphics system PyMol. Conclusions: GenePainter is a tool to analyse gene structure conservation providing various visualization options. A stable version of GenePainter for all operating systems as well as documentation and example data are available at http://www.motorprotein.de/genepainter.html."],["dc.identifier.doi","10.1186/1471-2105-14-77"],["dc.identifier.isi","000316396200001"],["dc.identifier.pmid","23496949"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8736"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30467"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","Najko"],["dc.relation.issn","1471-2105"],["dc.relation.orgunit","Fakultät für Mathematik und Informatik"],["dc.rights","CC BY 2.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/2.0"],["dc.title","GenePainter: a fast tool for aligning gene structures of eukaryotic protein families, visualizing the alignments and mapping gene structures onto protein structures"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","278"],["dc.bibliographiccitation.journal","BMC Bioinformatics"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Keller, Oliver"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Stanke, Mario"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Waack, Stephan"],["dc.date.accessioned","2018-11-07T11:14:00Z"],["dc.date.available","2018-11-07T11:14:00Z"],["dc.date.issued","2008"],["dc.description.abstract","Background: For many types of analyses, data about gene structure and locations of non-coding regions of genes are required. Although a vast amount of genomic sequence data is available, precise annotation of genes is lacking behind. Finding the corresponding gene of a given protein sequence by means of conventional tools is error prone, and cannot be completed without manual inspection, which is time consuming and requires considerable experience. Results: Scipio is a tool based on the alignment program BLAT to determine the precise gene structure given a protein sequence and a genome sequence. It identifies intron-exon borders and splice sites and is able to cope with sequencing errors and genes spanning several contigs in genomes that have not yet been assembled to supercontigs or chromosomes. Instead of producing a set of hits with varying confidence, Scipio gives the user a coherent summary of locations on the genome that code for the query protein. The output contains information about discrepancies that may result from sequencing errors. Scipio has also successfully been used to find homologous genes in closely related species. Scipio was tested with 979 protein queries against 16 arthropod genomes ( intra species search). For cross- species annotation, Scipio was used to annotate 40 genes from Homo sapiens in the primates Pongo pygmaeus abelii and Callithrix jacchus. The prediction quality of Scipio was tested in a comparative study against that of BLAT and the well established program Exonerate. Conclusion: Scipio is able to precisely map a protein query onto a genome. Even in cases when there are many sequencing errors, or when incomplete genome assemblies lead to hits that stretch across multiple target sequences, it very often provides the user with the correct determination of intron-exon borders and splice sites, showing an improved prediction accuracy compared to BLAT and Exonerate. Apart from being able to find genes in the genome that encode the query protein, Scipio can also be used to annotate genes in closely related species."],["dc.identifier.doi","10.1186/1471-2105-9-278"],["dc.identifier.isi","000257653900001"],["dc.identifier.pmid","18554390"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8427"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/54028"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Biomed Central Ltd"],["dc.relation.issn","1471-2105"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]