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Variation in the Human Leukocyte Antigen (HLA) gene system is very important. It is one of the most polymorphic regions of the human genome and one of the most extensively studied regions due to its association with autoimmune, infectious, and inflammatory diseases, such as rheumatoid arthritis, celiac disease, multiple sclerosis and Type I diabetes. The HLA gene system also plays a crucial role in...
An important task of aging research is to find genes that regulate lifespan. Wet-lab identification of aging genes is tedious and labor-intensive activity. Developing an algorithm to predict aging genes will be greatly helpful. In this paper, we systematically analyzed topological features of proteins encoded by Drosophila melanogaster aging genes versus those encoded by non-aging genes in protein-protein...
This paper presents a methodology for running NGS read mapping tools in the cloud environment based on the MapReduce programming paradigm. As a demonstration, the recently developed and robust sequence alignment tool, BFAST, is used within our methodology to handle massive datasets. The results of our experiments show that the transformation of existing read mapping tools to run within the MapReduce...
Cancer cells inefficiently produce energy through glycolysis even in ample oxygen, a phenomenon known as “aerobic glycolysis”. A characteristic of the rapid and incomplete catabolism of glucose is the secretion of lactate. Genome-scale metabolic models have been recently employed to describe the glycolytic phenotype of highly proliferating human cancer cells. Genome-scale models describe genotype-phenotype...
While workflow technology has gained momentum in the last decade as a means for specifying and enacting computational experiments in modern science, reusing and repurposing existing workflows to build new scientific experiments is still a daunting task. This is partly due to the difficulty that scientists experience when attempting to understand existing workflows, which contain several data preparation...
The recent advances made in high throughput genomic sequencing allow researchers to accurately determine the genetic make-up of an individual. Sharing this data across research institutes has proven to be challenging as the amount of data and available bandwidth cause large delays. Here, we present a network of dynamic lightpaths dedicated to the life sciences which connects research groups within...
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference...
Breakthroughs in technology that deliver fast and accurate molecular biology data, together with the use of advanced software, and analytical methods made possible quantitative accumulation of biological information leading to a qualitative evolution. Sequencing of human genome was of the first door to the era of systemic understanding in life sciences. The paper reviews the emerging concepts of systems...
Neural tube defects (NTDs) are common, severe congenital malformations. Gene BRCAl encodes a nuclear phosphoprotein that has a role in maintaining genomic stability, and it also acts as a tumor suppressor. Inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) is a key regulatory enzyme at the branch point for the synthesis of inositol hexakisphosphate (IP6), an intracellular signaling molecule. Both genes...
Due to the development of World Wide Web technologies, people are living in the place flooding trillions of web pages in every moment. The amount of web size has been increasing dramatically. For this reason, it is getting more difficult to find relevant web documents corresponding to what users want to read. Classifying documents into predefined categories is one of the most important tasks in Natural...
Motifs comparison plays a key role in clustering of redundant motifs and mapping motifs to transcription factors from previously characterized motif databases. Most of existed algorithms decompose the similarity of two motifs into the sum of similarities of aligned positions using position-independence assumption. However it is unreasonable to compare two motifs with vast difference in length. In...
Ribosomal protein L10A is a component of the 60S large ribosomal subunit. To explore the structure feature of RPL10A gene of the Ailuropoda melanoleuca,the cDNA and the genomic sequence of RPL10A gene were cloned using RT-PCR and touchdown -PCR technology. The obtained cDNA of RPL10A in giant panda is 689 bp in size, containing an ORF of 654 bp, and the deduced protein was composed of 217 amino acids...
40S ribosomal protein S10 is a protein encoded by the RPS10 gene in human, belonging to the S10E family of ribosomal proteins. To explore the structure characteristic of this gene of Ailuropoda melanoleuca, primers were designed based on the known nucleotide sequence of RPS10 gene. The RT-PCR and PCR strategy were employed to isolate cDNA and genome of RPS10 from A. melanoleuca respectively, followed...
The need for sequencing DNA has been growing tremendously over the past few years. Current next-generation sequencing techniques produce huge amounts of data but time and money remain limiting factors for researchers. Given a DNA sample, it is essential to produce a sufficient number of reads to create or recreate a digital representation of the DNA while minimizing the needed resources. This work...
This report showed some physico-chemical properties and structural features about UL41 protein predicted by some software and on-line tools. The analysis showed both the signal peptide and the trans membrance region are not found. Meanwhile, the protein has twenty-four potential phosphorylation sites. In addition, the protein has more hydrophilic amine acid districts than hydrophobic districts and...
The Duck Plague Virus (DPV) is the causative agent of Duck plague, which causes significant economic losses in the commercial duck industry all over the world. Our laboratory had identified and sequenced the DPV UL41 gene. Bioinformatics analysis of DPV UL41 gene were performed by some software and online tools. The results showed that GC content of duck plague virus UL41 gene was 42.42%, which encoded...
Fast alignment of small sequences to a very large sequence has recently been under attention of many researchers, due to the applications in processing the biological sequences and specially mapping the short reads of Next Generation Sequencing to an already assembled reference genome. The MEMOCODE 2012 contest was aimed to design a very efficient exact DNA sequence matching method to map a huge number...
The MEMOCODE design contest for 2012 is exact substring matching: a simplified form of the DNA sequence alignment problem. The challenge is to efficiently locate millions of 100-base-pair short read sequences in a 3-million-base-pair reference genome. Contestants had a month to create a fast system that ran on a given set of test data. Entries were judged both on absolute time and the product of time...
RNA-seq has the potential to discover genes created by complex chromosomal rearrangements. 'Fusion' genes formed by the breakage and re-joining of two different chromosomes have repeatedly been implicated in the development of cancer. However, although RNA-seq can detect these fusion events, normal cells are also characterized by read-through fusions across adjacent genes in the genome, or by transcription-induced...
Control of finite-valued networks, including Boolean networks, is currently a hot topic. In this paper the optimization control of the networks with present value performance criterion is discussed. The problem is formulated as a finite strategy game between human and machine. It is firstly proved that the optimal strategy can be found in the set of periodic strategies, which makes the problem finitely...
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