ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins... more
ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the
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Research Interests: Computational Biology, User Interface, Database Management Systems, Biological Sciences, Environmental Sciences, and 11 moreWeb Technology, Primer design, Polymerase Chain Reaction, Nucleic Acids, Computer User Interface Design, Molecular cloning, Source Code, Base Sequence, Open Architecture, Internet, and Web Interface
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Research Interests: Computer Graphics, Biological Sciences, Software, Phylogeny, Software Design, and 17 moreEnvironmental Sciences, Sequence alignment, Statistical Significance, Phylogenetic analysis, Nucleic Acids, Proteins, Genome Annotation, Protein Sequence Analysis, Protein Complex Detection, Protein Domains, Phylogenetic Tree, Amino Acid Profile, Multiple Sequence Alignment, Amino Acid Substitution Rates, Internet, Nucleotides, and Domain Structure
Current protein sequence databases employ different classification schemes that often provide conflicting annotations, especially for poorly characterized proteins. ProGMap (Protein Group Mappings, http://www.bioinformatics.nl/progmap) is... more
Current protein sequence databases employ different classification schemes that often provide conflicting annotations, especially for poorly characterized proteins. ProGMap (Protein Group Mappings, http://www.bioinformatics.nl/progmap) is a web-tool designed to help researchers and database annotators to assess the coherence of protein groups defined in various databases and thereby facilitate the annotation of newly sequenced proteins. ProGMap is based on a non-redundant dataset of over 6.6 million protein sequences which is mapped to 240,000 protein group descriptions collected from UniProt, RefSeq, Ensembl, COG, KOG, OrthoMCL-DB, HomoloGene, TRIBES and PIRSF. ProGMap combines the underlying classification schemes via a network of links constructed by a fast and fully automated mapping approach originally developed for document classification. The web interface enables queries to be made using sequence identifiers, gene symbols, protein functions or amino acid and nucleotide sequences. For the latter query type BLAST similarity search and QuickMatch identity search services have been incorporated, for finding sequences similar (or identical) to a query sequence. ProGMap is meant to help users of high throughput methodologies who deal with partially annotated genomic data.
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Research Interests: Algorithms, Machine Learning, Support Vector Machines, Benchmarking, Logistic Regression, and 19 moreInformation, Random Forest, BLAST, Nearest Neighbor, Protein structure, Biochemical, Proteins, Cross Validation, Support vector machine, Protein Sequence Analysis, Concept Hierarchy, Protein Domains, Random sampling, Protein Classification, Database, Artificial Neural Network, Hierarchical Classification, Biochemistry and cell biology, and DNA sequence
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Seed performance after dispersal is highly dependent on parental environmental cues, especially during seed formation and maturation. Here we examine which environmental factors are the most dominant in this respect and whether their... more
Seed performance after dispersal is highly dependent on parental environmental cues, especially during seed formation and maturation. Here we examine which environmental factors are the most dominant in this respect and whether their effects are dependent on the genotypes under investigation. We studied the influence of light intensity, photoperiod, temperature, nitrate, and phosphate during seed development on five plant attributes and thirteen seed attributes, using 12 Arabidopsis genotypes that have been reported to be affected in seed traits. As expected, the various environments during seed development resulted in changed plant and/or seed performances. Comparative analysis clearly indicated that, overall, temperature plays the most dominant role in both plant and seed performance, whereas light has a prominent impact on plant traits. In comparison to temperature and light, nitrate mildly affected some of the plant and seed traits while phosphate had even less influence on thos...