Geometric Aspects of Biological Sequence Comparison

Geometric Aspects of Biological Sequence Comparison

We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets of biosequences. The distances considered are more general than traditional generalized string edit dist...

Algorithmic Aspects of Heterogeneous Biological Networks Comparison

Following the innovative approach proposed in [3], we investigate the complexity of comparing two biological networks of different types – and thus, possibly differently modeled. More precisely, we consider the decomposition problem (either covering or partitioning) of one of the networks into Directed Acyclic Graphs (DAGs) with the extra requirement that, for each of these DAGs, there exists a...

A comparison study on some biological aspects of Platycephalus indicus in coastal waters of Bandar Abbas

Study was conducted to determine some biological characteristics and population dynamic of Platycephalus indicus were studied during one year from May 2011 to March 2012 in the coastal waters of Bandar Abbas. A total of 1106 samples were collected. Also, each month 35 fish was chosen and transferred to the laboratory for evaluation of spawning season. The ages of 279 specimens were determine...

Biological Sequence Comparison: An Overview of Techniques

Dedicated Hardware for Biological Sequence Comparison

Biological sequence comparison is a time consuming task on a Von Neuman computer. The addition of dedicated hardware for parallelizing the comparison algorithms results in a reduction of several orders of magnitude in the execution time. This paper presents and compares different dedicated approaches, based on the parallelization of the algorithms on linear arrays of processors.