Bioinformatics Softwares,Concepts,Articles,Career & More

Category archive

Sequence Analysis

Simulated sequence alignment software: An alternative to MSA benchmarks

in Algorithms/Databases/Sequence Analysis/Softwares/Tools by

In our previous article, we discussed different multiple sequence alignment (MSA) benchmarks to compare and assess the available MSA programs. However, since last decade, several sequence simulation software have been introduced and are gaining more interest. In this article, we will be discussing various sequence simulating software being used as alternatives to MSA benchmarks. Continue reading “Simulated sequence alignment software: An alternative to MSA benchmarks” »

Benchmark databases for multiple sequence alignment: An overview

in Algorithms/Sequence Analysis/Softwares by

Multiple sequence alignment (MSA) is a very crucial step in most of the molecular analyses and evolutionary studies. Many MSA programs have been developed so far based on different approaches which attempt to provide optimal alignment with high accuracy. Basic algorithms employed to develop MSA programs include progressive algorithm [1], iterative-based [2], and consistency-based algorithm [3]. Some of the programs incorporate several other methods into the process of creating an optimal alignment such as M-COFFEE [4] and PCMA [5]. Continue reading “Benchmark databases for multiple sequence alignment: An overview” »

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” »

1 2 3 5
Go to Top