# Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices

@article{Agrawal2011PairwiseSS, title={Pairwise Statistical Significance of Local Sequence Alignment Using Sequence-Specific and Position-Specific Substitution Matrices}, author={Ankit Agrawal and Xiaoqiu Huang}, journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, year={2011}, volume={8}, pages={194-205} }

Pairwise sequence alignment is a central problem in bioinformatics, which forms the basis of various other applications. Two related sequences are expected to have a high alignment score, but relatedness is usually judged by statistical significance rather than by alignment score. Recently, it was shown that pairwise statistical significance gives promising results as an alternative to database statistical significance for getting individual significance estimates of pairwise alignment scores…

## 40 Citations

Sequence-specific sequence comparison using pairwise statistical significance.

- BiologyAdvances in experimental medicine and biology
- 2011

This chapter presents a summary of recent advances in accurately estimating statistical significance of pairwise local alignment for the purpose of identifying related sequences, by making the sequence comparison process more sequence specific.

Derived distribution points heuristic for fast pairwise statistical significance estimation

- Computer ScienceBCB '10
- 2010

A simple heuristic is proposed, called the Derived Distribution Points (DDP) heuristic, which is designed taking into account the features of the pairwise statistical significance estimation procedure, and has shown to significantly improve the quality of pairwise statistics significance estimates (evaluated in terms of retrieval accuracy) even when using low values of N.

MPIPairwiseStatSig: parallel pairwise statistical significance estimation of local sequence alignment

- Computer ScienceHPDC '10
- 2010

This paper presents a parallel algorithm for pairwise statistical significance estimation, called MPIPairwiseStatSig, implemented in C using MPI, and Distributing the most compute-intensive portions of the pairwise statistics significance estimation procedure across multiple processors has been shown to result in near-linear speed-ups for the application.

Par-PSSE: Software for Pairwise statistical significance estimation in parallel for local sequence alignment

- Computer Science
- 2012

This paper presents a software library for estimating pairwise statistical significance in parallel, named Par-PSSE, implemented in C++ using OpenMP, MPI paradigms and their hybrids, and applies the parallelization technique to estimate non-conservative PSS using standard, sequence-specific, and position-specific substitution matrices.

Protein sequence alignment with family-specific amino acid similarity matrices

- Biology, Computer ScienceBMC Research Notes
- 2011

The results of this work indicate that using family-specific similarity matrices significantly improves the quality of the alignment of homologous sequences over the traditional sequence alignment based on a single general-purpose similarity matrix.

FPGA architecture for pairwise statistical significance estimation

- Computer ScienceInt. J. High Perform. Syst. Archit.
- 2013

This work develops algorithms for sequence-specific strategies for hardware acceleration of pairwise sequence alignment in conjunction with statistical significance estimation, and provides a 'flexible array' hardware architecture which provides a scalable systolic array suitable for both long and short sequences.

Parallel pairwise statistical significance estimation of local sequence alignment using Message Passing Interface library

- Computer ScienceConcurr. Comput. Pract. Exp.
- 2011

This paper presents a parallel algorithm for pairwise statistical significance estimation, called MPIPairwiseStatSig, implemented in C using MPI library, and applies the parallelization technique to estimate non‐conservative pair wise statistical significance using standard, sequence‐specific, and position‐specific substitution matrices.

Enhancing Parallelism of Pairwise Statistical Significance Estimation for Local Sequence Alignment

- Computer Science
- 2011

This paper evaluates the use of OpenMP, MPI and hybrid paradigms to accelerate the estimation of PSS of local sequence alignment and achieves a speedup of up to 113.10× using 128 cores.

PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment using weighted biochemical properties of amino acids

- Computer Science, BiologyBMC Research Notes
- 2015

PR2ALIGN will be helpful for researchers who wish to align amino acid sequences by using flexible user-specified alignment scoring functions based on the biochemical properties of amino acids instead of the amino acid substitution matrix.

Chapter 3 Mining Genomic Sequence Data for Related Sequences Using Pairwise Statistical Significance

- Biology, Computer Science
- 2013

This chapter presents the algorithm of pairwise statistical significance, then describes several high performance algorithms, which enable significant acceleration of pair wise statistical significance estimation.

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