SAliBASE: A Database of Simulated Protein Alignments

Abstract

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.