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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian

Haim Ashkenazy¹, Eli Levy Karin^1,2, Zach Mertens³

¹Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Nucleic Acids Research

|May 2, 2017

Summary

This summary is machine-generated.

SpartaABC infers insertion and deletion (indel) parameters from sequence data, enabling more accurate biological simulations. This tool helps researchers select appropriate indel parameters for sequence analysis and simulation studies.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Genetics

Background:

Multiple sequence alignments are crucial for biological analyses.
Parametric bootstrap procedures using sequence simulators are common for studying alignment results.
A key challenge is selecting appropriate insertion and deletion (indel) parameters for simulations to accurately reflect biological data.

Purpose of the Study:

To present SpartaABC, a novel web server designed to infer indel parameters from sequence data.
To provide users with a method for choosing indel parameters that generate biologically realistic sequences.
To facilitate more accurate sequence simulation studies.

Main Methods:

SpartaABC employs an approximate Bayesian computation (ABC) rejection algorithm.
The server extracts summary statistics from input sequence data.
It performs numerous sequence simulations with randomly sampled indel parameters and retains those yielding statistics close to the input data.

Main Results:

SpartaABC provides point estimates and approximate posterior distributions for indel parameters.
The server integrates Dawg 2.0 and INDELible for sequence simulation with inferred parameters.
Differences in indel dynamics were demonstrated across three protein-coding genes in mammalian orthologs.

Conclusions:

SpartaABC addresses the critical need for selecting appropriate indel parameters in sequence simulation.
The tool enhances the reliability of phylogenetic and evolutionary analyses.
It offers a valuable resource for researchers in bioinformatics and evolutionary biology.