Affiliation: Stockholm University
- Orthology confers intron position conservationAnna Henricson
Department of Cell and Molecular Biology, Karolinska Institutet, SE 17177 Stockholm, Sweden
BMC Genomics 11:412. 2010..Therefore, we wanted to investigate whether orthologs have a higher degree of intron position conservation (IPC) compared to non-orthologous sequences that are equally similar in sequence...
- Domain architecture conservation in orthologsKristoffer Forslund
Stockholm Bioinformatics Centre, Science for Life Laboratory, Box 1031, Solna, 17121 Sweden
BMC Bioinformatics 12:326. 2011..We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs...
- Predicting protein function from domain contentKristoffer Forslund
Stockholm Bioinformatics Centre, Stockholm University, 10691 Stockholm, Sweden
Bioinformatics 24:1681-7. 2008..The relationship between protein domain content and function is important to investigate, to understand how domain combinations encode complex functions...
- Benchmarking homology detection procedures with low complexity filtersKristoffer Forslund
Stockholm Bioinformatics Center, Stockholm University, SE 10691 Stockholm, Sweden
Bioinformatics 25:2500-5. 2009..A common benchmark for homology detection procedures is to use SCOP/ASTRAL domain sequences belonging to the same or different superfamilies, but these contain almost no low complexity sequences...
- InParanoid 7: new algorithms and tools for eukaryotic orthology analysisGabriel Ostlund
Department of Biochemistry and Biophysics, Stockholm Bioinformatics Centre, AlbaNova University Centre, Stockholm University, SE 10691 Stockholm, Sweden
Nucleic Acids Res 38:D196-203. 2010..To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters...
- Evolution of protein domain architecturesKristoffer Forslund
Stockholm Bioinformatics Centre, Stockholm University, Stockholm, Sweden
Methods Mol Biol 856:187-216. 2012..Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly)...
- OrthoDisease: tracking disease gene orthologs across 100 speciesKristoffer Forslund
Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, AlbaNova, 10691 Stockholm, Sweden
Brief Bioinform 12:463-73. 2011..We found large-scale support for this hypothesis as significantly fewer duplications were observed for disease genes in the OrthoDisease ortholog groups...
- Domain tree-based analysis of protein architecture evolutionKristoffer Forslund
Stockholm Bioinformatics Centre, AlbaNova, Stockholm University, Stockholm, Sweden
Mol Biol Evol 25:254-64. 2008..However, no strong functional bias was found in architectures with multiple origins...
- Benchmarking the next generation of homology inference toolsGanapathi Varma Saripella
Science for Life Laboratory, Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE 10691, Sweden
Bioinformatics 32:2636-41. 2016....
- The Pfam protein families databaseRobert D Finn
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SA, UK
Nucleic Acids Res 36:D281-8. 2008..sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/), as well as from mirror sites in France (http://pfam.jouy.inra.fr/) and South Korea (http://pfam.ccbb.re.kr/)...
- A novel exploratory method for visual recombination detectionKorbinian Strimmer
Department of Statistics, University of Munich, Germany
Genome Biol 4:R33. 2003..To illustrate the method, simulated data and HIV-1 and influenza A datasets are investigated...