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Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

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Updated: Nov 26, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Fast and Accurate Multiple Sequence Alignment with MSAProbs-MPI.

Jorge González-Domínguez¹

¹Computer Architecture Group, Universidade da Coruña, CITIC, A Coruña, Spain. jorge.gonzalezd@udc.es.

Methods in Molecular Biology (Clifton, N.J.)

|December 8, 2020

Summary

This summary is machine-generated.

MSAProbs-MPI is a tool that accurately aligns large biological sequence datasets quickly. It uses high-performance computing on multicore clusters to overcome computational challenges in bioinformatics.

Keywords:

High-performance computing MSAProbs-MPI Message passing interface Multiple sequence alignment Multithreading Parallel computing

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Area of Science:

Bioinformatics and Computational Biology
High-Performance Computing

Background:

Multiple sequence alignment (MSA) is fundamental for many biological analyses.
Existing MSA methods struggle with large datasets due to high computational demands.
There is a need for efficient and accurate MSA tools for big data.

Purpose of the Study:

To explain the statistical and biological principles behind MSAProbs-MPI.
To detail the high-performance computing techniques accelerating MSAProbs-MPI.
To provide guidance on optimizing MSAProbs-MPI for high-performance execution.

Main Methods:

Utilizes statistical and biological models for sequence alignment.
Employs Message Passing Interface (MPI) for parallel processing on multicore clusters.
Leverages high-performance computing (HPC) strategies for speed optimization.

Main Results:

MSAProbs-MPI achieves highly accurate alignments.
The tool demonstrates a relatively short runtime even for large datasets.
Exploits multicore cluster hardware for significant performance gains.

Conclusions:

MSAProbs-MPI offers an effective solution for large-scale multiple sequence alignment.
The combination of advanced algorithms and HPC techniques enhances efficiency.
Proper configuration ensures optimal performance for demanding bioinformatics tasks.