Parallelized multiple alignment.
TL;DR: Parallel processing functionality in the form of single-instruction multiple-data (SIMD) technology was implemented into the multiple alignment program Praline by using 'message passing interface' (MPI) routines.
read more
Abstract: Summary: Multiple sequence alignment is a frequently used technique for analyzing sequence relationships. Compilation of large alignments is computationally expensive, but processing time can be considerably reduced when the computational load is distributed over many processors. Parallel processing functionality in the form of singleinstruction multiple-data (SIMD) technology was implemented into the multiple alignment program Praline by using ‘message passing interface’ (MPI) routines. Over the alignments tested here, the parallelized program performed up to ten times faster on 25 processors compared to the single processor version. Availability: Example program code for parallelizing pairwise alignment loops is available from http://mathbio.nimr. mrc.ac.uk/∼jkleinj/tools/mpicode. The ‘message passing interface’ package (MPICH) is available from http:/www.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan,Ira M. Hall +1 more
- 28 Jan 2010
TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, BEDTools, which allows the user to compare large datasets with both public and custom genome annotation tracks.
12.3K
Parallelization of the MAFFT multiple sequence alignment program
Kazutaka Katoh,Hiroyuki Toh +1 more
TL;DR: The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library to reduce the time required for large-scale sequence analyses.
A Quick Guide for Developing Effective Bioinformatics Programming Skills
TL;DR: The following set of guidelines distill several key principals of effective bioinformatics programming, which the authors learned through insights gained across many years of combined experience developing popular bio informatics software applications and database systems in both academic and commercial settings.
Software Note: The PRALINE online server: optimising progressive multiple alignment on the web
V. A. Simossis,Jaap Heringa +1 more
TL;DR: The online server for PRALINE is introduced, an iterative versatile progressive multiple sequence alignment (MSA) tool that provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided alignment and a reliability measure for aligned individual residue positions.
66
Multiple sequence alignment in parallel on a workstation cluster
Justin Ebedes,Amitava Datta +1 more
TL;DR: It is shown that parallelizing the ClustalW algorithm can result in significant speedup, and experimental results show that speedup of over 5.5 on six processors is obtainable for most inputs.
62
References
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
TL;DR: A new method for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives but avoids the most serious pitfalls caused by the greedy nature of this algorithm.
7.5K
A high-performance, portable implementation of the MPI message passing interface standard
William Gropp,Ewing Lusk,Nathan E. Doss,Anthony Skjellum +3 more
- 01 Sep 1996
TL;DR: The MPI Message Passing Interface (MPI) as mentioned in this paper is a standard library for message passing that was defined by the MPI Forum, a broadly based group of parallel computer vendors, library writers, and applications specialists.
2.4K
Progressive sequence alignment as a prerequisite to correct phylogenetic trees.
Da-Fei Feng,Russell F. Doolittle +1 more
TL;DR: A progressive alignment method that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship is described.
2.1K
Portable implementation of the mpi message passing interface standard
William Gropp,Ewing Lusk,Nathan E. Doss,A. Skjeltum. A Highperformance +3 more
- 01 Jan 1996
TL;DR: The MPI Message Passing Interface (MPI) as discussed by the authors is a standard library for message passing that was defined by the MPI Forum, a broadly based group of parallel computer vendors, library writers, and applications specialists.
2K