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.artnumber","265"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Research Notes"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Hatje, Klas"],["dc.contributor.author","Keller, Oliver"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Pillmann, Holger"],["dc.contributor.author","Waack, Stephan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-09T11:53:04Z"],["dc.date.available","2019-07-09T11:53:04Z"],["dc.date.issued","2011"],["dc.description.abstract","Background Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons. Results Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools. Conclusions With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio outperforms all other software tested. WebScipio has been restructured and provides easy access to the genome assemblies of about 640 eukaryotic species. Scipio and WebScipio are freely accessible at http://www.webscipio.org."],["dc.identifier.doi","10.1186/1756-0500-4-265"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/6873"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60336"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["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.subject.ddc","510"],["dc.title","Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]