The performances of PFP, ESG, and PSI-BLAST in predicting the functional diversity of moonlighting proteins were analyzed. PFP shows overall better performance in predicting diverse moonlighting functions as compared with PSI-BLAST and ESG. Recall by PSI-B...
BACKGROUND: A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpre...
Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the...
Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more exp...
In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported...
Experimentally determined protein tertiary structures are rapidly accumulating in a database, partly due to the structural genomics projects. Included are proteins of unknown function, whose function has not been investigated by experiments and was not abl...
Argininosuccinate Synthase Binding Sites Biochemistry Bioinformatics Computer Simulation Molecular Biosciences Protein Structure Sensitivity and Specificity Tertiary Tetrahydrofolate Dehydrogenase/chemistry
Computational methods for de novo identification of gene regulation elements, such as transcription factor binding sites, have proved to be useful for deciphering genetic regulatory networks. However, despite the availability of a large number of algorithm...
Algorithms Base Sequence Binding Sites Biochemistry Bioinformatics Computational Biology / Methods DNA/Chemistry DNA/methods Escherichia coli/Genetics Factors/Metabolism Markov Chains Markov Chains Regulatory Sequences Molecular Biosciences Regulon Sequence Alignment Sequence Analysis
In the human genome, regulatory signals are dispersed in DNA sequences and segments that control gene expression. We have developed a computational model to localize the position of potential regulatory signals in human genomic DNA. In this publication...
Binding-site Biochemistry Bioinformatics Codes in Human DNA DNASE-I hypersensitive sites Gene Regulation Genetic Vocabulary Human Genome Hypersensitive Sites Molecular Biosciences Promoter Regions Regulatory Signals Sequence Context Transcription factor binding sites Transcription Factors
The human genome may include overlapping codes to accommodate a wide-range of selective pressures imposed by various cellular requirements. In this context, we have examined whether occurrences of MLL1 morphemes in exons of human genes may impose constrai...
Biochemistry Bioinformatics Chemistry Coding sequences Codon bias Codon selection Codon utilization CpG islands Exon Exons Genomics Human Genome MLL1 morphemes in CDSs MLL1 morphemes in exons Morphemes MLL1 Overlapping codes Regulatory codes in DNA Trithorax response elements
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