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As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are(More)
UNLABELLED We present a web server to predict the functional effect of single or multiple amino acid substitutions, insertions and deletions using the prediction tool PROVEAN. The server provides rapid analysis of protein variants from any organisms, and also supports high-throughput analysis for human and mouse variants at both the genomic and protein(More)
Information theory traditionally deals with “conventional data,” be it textual data, image, or video data. However, databases of various sorts have come into existence in recent years for storing “unconventional data” including biological data, social data, web data, topographical maps, and medical data. In compressing such data,(More)
Traditionally, the performance of distributed algorithms has been measured in terms of time and message complexity. Message complexity concerns the number of messages transmitted over all the edges during the course of the algorithm. However, in energy-constraint radio or wireless networks (e.g., sensor networks), energy is a critical factor in measuring(More)
F. Brooks argues in [3] there is “no theory that gives us a metric for information embodied in structure” Shannon himself alluded to it fifty years earlier in his little known 1953 paper [14]. Indeed, in the past information theory dealt mostly with “conventional data,” be it textual data, image, or video data. However, databases(More)
Traditionally, the performance of distributed algorithms has been measured in terms of running time and message complexity. However, in many settings, a more accurate and relevant measure of performance is required. In ad hoc wireless networks, energy is a very critical factor for measuring the efficiency of a distributed algorithm. Thus in addition to the(More)
Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference genome, limiting our understanding of gene order and content. A consensus representation of multiple genomes will provide a better(More)
Recently we have developed a new algorithm, PROVEAN (<u>Pro</u>tein <u>V</u>ariation <u>E</u>ffect <u>An</u>alyzer), for predicting the functional effect of protein sequence variations, including single amino acid substitutions and small insertions and deletions [2]. The prediction is based on the change,(More)
Constrained sequences find applications in communication, magnetic recording, and biology. In this paper, we restrict our attention to the so-called (d, k) constrained binary sequences in which any run of zeros must be of length at least d and at most k, where 0lesd<k. In some applications one needs to know the number of occurrences of a given pattern w(More)
The comprehensive identification of functional transcription factor binding sites (TFBSs) is an important step in understanding complex transcriptional regulatory networks. This study presents a motif-based comparative approach, STAT-Finder, for identifying functional DNA binding sites of STAT3 transcription factor. STAT-Finder combines STAT-Scanner, which(More)