Bioinformatics Softwares,Concepts,Articles,Career & More

Category archive

Sequence Analysis

SparkBLAST: Introduction

in Algorithms/Cloud Computing/Sequence Analysis by

The basic local alignment search tool (BLAST) [1,2] is known for its speed and results, which is also a primary step in sequence analysis. The ever increasing demand of processing huge amount of genomic data has led to the development of new scalable and highly efficient computational tools/algorithms. For example, MapReduce is the most widely accepted framework which supports design patterns representing general reusable solutions to some problems including biological assembly [3] and is highly efficient to handle large datasets running over hundreds to thousands of processing nodes [4]. But the implementation frameworks of MapReduce (such as Hadoop) limits its capability to process smaller data. Continue reading “SparkBLAST: Introduction” »

Role of Information Theory, Chaos Theory, and Linear Algebra and Statistics in the development of alignment-free sequence analysis

in Algorithms/Sequence Analysis/Softwares by

Sequence alignment is a customary to not only find similar regions among a pair of sequences but also to study the structural, functional and evolutionary relationship between organisms. Many tools have been discovered to achieve the goal of alignment of a pair of sequences, separately for nucleotide sequence and amino acid sequence, BLOSSUM & PAM [1] are a few to name. Continue reading “Role of Information Theory, Chaos Theory, and Linear Algebra and Statistics in the development of alignment-free sequence analysis” »

A short introduction to protein structures modification and ModFinder

in Sequence Analysis/Softwares/Tools by

A lot of protein structures are determined on a large scale and submitted in Protein Data Bank (PDB) www.rcsb.org [1]. After the experimental determination of these structures, they are used in many scientific studies and experiments are performed upon them such as mutagenesis, docking, and so on. Continue reading “A short introduction to protein structures modification and ModFinder” »

1 2 3 4
Go to Top