Sequence-based learning algorithms for understanding and improving protein characteristics

The development of high-throughput measurement techniques resulted in rapidlyincreasing amounts of biological data, which made computational methodsessential for biological research. Hence, the field of bioinformatics emergedthat since plays an important role in storing, making accessible, integrating,and analysing different types of biological...

Insight into neutral and disease-associated human genetic variants through interpretable predictors

A variety of methods that predict human nonsynonymous single nucleotide polymorphisms (SNPs) to be neutral or disease-associated have been developed over the last decade. These methods are used for pinpointing disease-associated variants in the many variants obtained with next-generation sequencing technologies. The high performances of current...

SPiCE: A web-based tool for sequence-based protein classification and exploration

Background Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software tools are available for both feature extraction and classifier construction, their application is not straightforward,...

Predicting functional effect of human missense mutations

Our aim is to prioritize human missense mutations by their probability of being disease causing. Such a computational method could be used to obtain a reduced set of mutations with a relatively large fraction of disease related mutations, thereby aiding in the search for this type of mutation within a large mutation set.<br/><br/>Whereas a range...

Exploring Sequence Characteristics Related to High- Level Production of Secreted Proteins in Aspergillus niger

Protein sequence features are explored in relation to the production of over-expressed extracellular proteins by fungi. Knowledge on features influencing protein production and secretion could be employed to improve enzyme production levels in industrial bioprocesses via protein engineering. A large set, over 600 homologous and nearly 2,000...

Proposal for an enzyme redesign method to improve production rates in Aspergillus niger

Relating sequence properties to protein secretion

Aspergillus niger is widely used for industrial enzyme production. Knowledge on high-level protein secretion could be useful to improve production rates. We used sequencebased classification methods to identify important properties<br/>for successful high-level secretion, which will be used to redesign proteins for improved secretion.

Logic gene network design: a software tool based on modularity and standardization