MP-Align: alignment of metabolic pathways

Alignment of metabolic pathways

MOTIVATION Several genome-scale efforts are underway to reconstruct metabolic networks for a variety of organisms. As the resulting data accumulates, the need for analysis tools increases. A notable requirement is a pathway alignment finder that enables both the detection of conserved metabolic pathways among different species as well as divergent metabolic pathways within a species. When compa...

Simple and Fast Alignment of Metabolic Pathways

Consistent alignment of metabolic pathways without abstraction.

Pathways show how different biochemical entities interact with each other to perform vital functions for the survival of organisms. Similarities between pathways indicate functional similarities that are difficult to identify by comparing the individual entities that make up those pathways. When interacting entities are of single type, the problem of identifying similarities reduces to graph is...

Alignment-Free Comparison of Metabolic Pathways

Classification of species is a fundamental problem in evolutionary studies. Most contributions to this field have been mainly based on the so-called “molecular approach”, that exploits polymorphism information in DNA or proteins to assess the phylogenetic relationship among species [9]. But it is widely agreed that, in this approach, the choice of sequences for comparison greatly affects the fi...

Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard [1] and heuristics are desgined for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics, that scale...