The science of bioinformatics has developed in the wake of methods to determine the sequences of the informational macromolecules--DNAs, RNAs and proteins. But in a wider sense, the biological world depends in its every process on the transmission of information, and hence bioinformatics is the fundamental core of biology. We here give a consideration of some of the key problems of bioinformati...

Pre-processing plays a vital role in cDNA-microarray data analysis. Without proper preprocessing it is likely that the biological conclusions will be misleading. However, there are many alternatives and in order to choose a proper pre-processing procedure it is necessary to understand the effect of different methods. This chapter discusses several pre-processing steps, including image analysis,...

This document surveys the computational strategies followed to parallelize the most used software in the bioinformatics arena. The studied algorithms are computationally expensive and their computational patterns range from regular, such as database searching applications, to very irregularly structured patterns (phylogenetic trees). Fineand coarse-grained parallel strategies are discussed for ...

Ap Applicati tions ons in in Pl Plant t Scien Sciences ces Increasingly, quantitative approaches to plant morphology are changing the landscape of research for plant ecology, physiology , and evolution. Advances in microscopy, imaging, and computational analyses potentially allow more detailed investigations than have previously been possible. This has increased the variety and quantity of data...

objective(s) staphylococcus aureus is a leading cause of many nosocomial and community acquired infections. according to many reports, antibiotic therapy can not guarantee the eradication of s. aureus infections. thus designing an adhesin based vaccine could restrain the s. aureus infections. this study designed for construction of a new fusion protein vaccine against s. aureus infections based...

Pathogens produce effectors that manipulate the host to the benefit of the pathogen. These effectors are often secreted proteins that are upregulated during the early phases of infection. These properties can be used to identify candidate effectors from genomes and transcriptomes of pathogens. Here we describe commonly used bioinformatic approaches that (1) allow identification of genes encodin...

Cellarium is a Computational Biology Workflowing Environment. It is designed to simplify the creation and refinement of workflows. There are a large variety of bioinformatic disparate components: data sources, algorithms, visualizations, etc.. Cellarium provides a means of leveraging any such component, providing greater interoperability of components than ad-hoc approaches. Cellarium also prov...

Multi-label classification is useful in many bioinformatics tasks such as gene function prediction and protein site localization. This paper presents an improved neural network algorithm, Max Label Distance Back Propagation Algorithm for Multi-Label Classification. The method was formulated by modifying the total error function of the standard BP by adding a penalty term, which was realized by ...

We outline our expectations for a new bioinformatic and neuroscience of therapeutic hypnosis, psychotherapy, and rehabilitation based on the Human Genome Project. Just as The Human Genome Project identified the psychobiological foundations of modern medicine with the new technology of sequencing DNA during the past decade, we propose extending this bioinformatic knowledge base with the technolo...

A hardware coprocessor for the rapid calculation of bioinformatic sequence alignments is presented. The coprocessor uses a globally-asynchronous locally-synchronous (GALS) design style which makes the coprocessor much easier to scale as CMOS feature sizes decrease. The coprocessor is intended to be implemented on a single integrated circuit along with a simple 32-bit RISC processor and memory s...