AI Article Synopsis
- Simulated alignments are a practical alternative to manual multiple sequence alignments, allowing researchers to evaluate alignment tools using sequences with known evolutionary histories.
- Creating these simulated sequences requires bioinformatics expertise and can be time-consuming, which is a hassle for users needing diverse datasets.
- The study's primary goal is to develop a database called SAliBASE, containing simulated protein sequences and their corresponding alignments, tailored with varying parameters to aid in evaluating multiple alignment methods.
Article 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343434 | PMC |
| http://dx.doi.org/10.1177/1176934318821080 | DOI Listing |
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