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A novel hybrid gene prediction method employing protein multiple sequence alignments
This work extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction.
Drawing the tree of eukaryotic life based on the analysis of 2,269 manually annotated myosins from 328 species
This approach is expected to result in superior accuracy compared to single-gene or phylogenomic analyses because the orthology problem is resolved and a strong determinant not depending on any technical uncertainties is incorporated, the class distribution.
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
- Oliver Keller, Florian Odronitz, M. Stanke, M. Kollmar, S. Waack
- BiologyBMC Bioinformatics
- 13 June 2008
Scipio is able to precisely map a protein query onto a genome and provides the user with the correct determination of intron-exon borders and splice sites, showing an improved prediction accuracy compared to BLAT and Exonerate.
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species
The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts.
Six Subgroups and Extensive Recent Duplications Characterize the Evolution of the Eukaryotic Tubulin Protein Family
Tubulins cannot be used for constructing species phylogenies without resolving their ortholog–paralog relationships, and the many gene duplicates and also the independent loss of the δ-, ε-, or ζ-tubulins suggest that tubulins can functionally substitute each other.
Evolution of the eukaryotic ARP2/3 activators of the WASP family: WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML
The analysis showed that the last common ancestor of the eukaryotes must have contained a homolog of WASP, WAVE, and WASH, and the recently identified WASH and WHAMM proteins.
Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins
The myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution, in contrast to other protein families, many myosins are still present in extant species.
Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution
- M. Kollmar
- BiologyMolecular biology and evolution
- 7 October 2016
The correlation of sequence and structural data suggests the single-headed class-8 and class-9 dyneins to localize to the distal end of the axonemal repeat and the class-7 dynein filling the region up to the proximal heterodimeric IAD, suggesting ongoing diversification and fine-tuning of flagellar functions in extant taxa and species.
WebScipio: An online tool for the determination of gene structures using protein sequences
- Florian Odronitz, Holger Pillmann, Oliver Keller, S. Waack, M. Kollmar
- BiologyBMC Genomics
- 18 September 2008
WebScipio is a tool that allows users to get a high-quality gene structure prediction from a protein query and produces predictions that are close to what can be achieved by manual annotation, for in-species and cross-species searches alike.
The landscape of human mutually exclusive splicing
Evidence is provided for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than five-fold and offers new insights into MXE splicing mechanics and evolution.