SAliBASE: A Database of Simulated Protein Alignments

Simulated alignments are alternatives to manually constructed multiple sequence alignments for evaluating performance of multiple sequence alignment tools. The importance of simulated sequences is recognized because their true evolutionary history is known, which is very helpful for reconstructing a...

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Bibliographic Details
Published in:Evolutionary Bioinformatics 2019, Vol.15, p.1176934318821080-1176934318821080
Main Authors: Pervez, Muhammad Tariq, Shah, Hayat Ali, Babar, Masroor Ellahi, Naveed, Nasir, Shoaib, Muhammad
Format: Article
Language:English
Subjects:
Alignment
Bioinformatics
Datasets
Deoxyribonucleic acid
DNA
Downloading
Gene deletion
Insertion
Nucleotide sequence
Performance evaluation
Phylogenetics
Phylogeny
Proteins
Sequences
Simulation
Software
Software or Database Review
Trees
Websites
Writers
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Description
Summary:Simulated alignments are alternatives to manually constructed multiple sequence alignments for evaluating performance of multiple sequence alignment tools. The importance of simulated sequences is recognized because their true evolutionary history is known, which is very helpful for reconstructing accurate phylogenetic trees and alignments. However, generating simulated alignments require expertise to use bioinformatics tools and consume several hours for reconstructing even a few hundreds of simulated sequences. It becomes a tedious job for an end user who needs a few datasets of variety of simulated sequences. Currently, there is no databank available which may help researchers to download simulated sequences/alignments for their study. Major focus of our study was to develop a database of simulated protein sequences (SAliBASE) based on different varying parameters such as insertion rate, deletion rate, sequence length, number of sequences, and indel size. Each dataset has corresponding alignment as well. This repository is very useful for evaluating multiple alignment methods.
ISSN:1176-9343
1176-9343
DOI:10.1177/1176934318821080