Background The schematic for every living organism is stored in long molecules known as chromosomes made of a substance known as DNA (deoxyribonucleic acid. Each cell in an organism has a complete copy of its DNA, also known as its genomewhich is conveniently modeled as a sequence of symbols (alternately referred to as nucleotides or bases) in the DNA alphabet {A,C,T,G}. In humans, and most mam...

The aim of this handout is to present you with some theoretical background that might be helpful for building phylogenetic trees. This handout also provides an step-by-step example of how to build a phylogenetic tree 1 .

Applying coding theory in genetic sequence analysis is a new research area for the information theory in biology. It has the potentioal to help the biologist to understand the nature of the living organisms and find the solutions to DNA computations. After an introduction of the biology, this paper reviewed the application of coding theory, especially error ,control theory, in sequence analysis...

When applying genome-wide sequencing technologies to disease investigation, it is increasingly important to resolve sequence variation in regions of the genome that may have homologous sequences. The human mitochondrial genome challenges interpretation given the potential for heteroplasmy, somatic variation, and homologous nuclear mitochondrial sequences (numts). Identical twins share the same ...

A genetic sequence is simply a way of representing DNA, RNA, and proteins by a character string, an unbroken sequence of letters. A sequence has a finite length and contains only those characters belonging to a specified alphabet. An alphabet is a set of allowable characters. DNA uses a 4-character alphabet that consists of {A,C,G,T}. Likewise RNA uses a 4-character alphabet {A,C,G,U}. Proteins...

This talk will review a little over a decade’s research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen since that time. The function of the models in biological sequence analysis is to summarize the information concerning what is known as a motif or a domain in...

This paper examines flow balance, a basic assumption used in the operational analysis of queues and other discrete-state systems. Violation of this assumption can lead to large errors in estimates of state occupancies and average performance measures. However. if the state occupancies of a state sequence are approximated using a subsequence, then the maximum and average errors are of the order ...

The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative forma...

Adaptive resonance theory (ART) describes a class of artiicial neural network architectures that act as classiication tools which self-organize, work in real-time, and require no retraining to classify novel sequences. We have adapted ART networks to provide support to scientists attempting to categorize tandem repeat DNA fragments from Onchocerca volvulus. In this approach, sequences of DNA fr...