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The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (È1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply(More)
Support vector machines (SVMs) have shown strong generalization ability in a number of application areas, including protein structure prediction. However, the poor comprehensibility hinders the success of the SVM for protein structure prediction. The explanation of how a decision made is important for accepting the machine learning technology, especially(More)
Information about local protein sequence motifs is very important to the analysis of biologically significant conserved regions of protein sequences. These conserved regions can potentially determine the diverse conformation and activities of proteins. In this work, recurring sequence motifs of proteins are explored with an improved K-means clustering(More)
Discovering protein sequence motif information is one of the most crucial tasks in bioinformatics research. In this paper, we try to obtain protein recurring patterns which are universally conserved across protein family boundaries. In order to achieve the goal, our dataset is extremely large. Therefore, an efficient technique is required. In this article,(More)
— Protein sequence motifs information is very important to the analysis of biologically significant regions. The conserved regions have the potential to determine the conformation, function and activities of the proteins. The main purpose of this paper is trying to obtain protein sequence motifs which are universally conserved and across protein family(More)
Hierarchical and k-means clustering are two major analytical tools for unsupervised microarray datasets. However, both have their innate disadvantages. Hierarchical clustering cannot represent distinct clusters with similar expression patterns. Also, as clusters grow in size, the actual expression patterns become less relevant. K-means clustering requires a(More)
Non-covalent and covalent homo-oligomerization of membrane proteins regulates their subcellular localization and function. Here, we described a novel oligomerization mechanism affecting solute carrier family 30 member 3/zinc transporter 3 (SLC30A3/ZnT3). Oligomerization was mediated by intermolecular covalent dityrosine bonds. Using mutagenized ZnT3(More)
The automatic prediction of protein three dimensional structures from its amino acid sequence has become one of the most important and researched fields in bioinformatics. As models are not experimental structures determined with known accuracy but rather with prediction it's vital to determine estimates of models quality. We attempt to solve this problem(More)