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Updated: Jul 9, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Portable BLAST-like algorithm library and its implementations for command line, Python, and R.

Steven Schmid¹, Aditya Jeevannavar², Timothy R Julian³

¹hakuna AG, Zürich, Switzerland.

|November 30, 2023

Summary

This summary is machine-generated.

A new tool, nsearch, offers portable, embeddable BLAST-like functionality for sequence similarity searches. It enables integration into R (Blaster) and Python (npysearch) applications, matching the speed and accuracy of existing BLAST tools.

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Published on: May 28, 2021

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Basic Local Alignment Search Tool (BLAST) is a standard for sequence similarity searches.
Current BLAST implementations are primarily command-line tools, limiting integration into diverse applications.
A need exists for portable, modular, and embeddable BLAST-like algorithms.

Purpose of the Study:

Introduce nsearch, a C++11 library and command-line tool providing embeddable BLAST-like functionality.
Demonstrate nsearch's portability through R (Blaster) and Python (npysearch) packages.
Facilitate the integration of sequence similarity searches into larger data science frameworks.

Main Methods:

Developed nsearch as a C++11 library and command-line tool.
Created Blaster for R and npysearch for Python, leveraging the nsearch library.
Conducted performance benchmarks comparing nsearch, Blaster, and npysearch against VSEARCH and BLAST+.

Main Results:

nsearch provides portable and embeddable BLAST-like sequence similarity search capabilities.
Blaster and npysearch packages successfully integrate nsearch into R and Python environments, respectively.
Benchmarks confirm nsearch, Blaster, and npysearch offer comparable speed and accuracy to established tools like VSEARCH and BLAST+.

Conclusions:

nsearch offers a flexible and efficient solution for embedding sequence similarity searches into various applications.
The development of Blaster and npysearch enhances accessibility for R and Python users.
Future implementations in languages like Julia are envisioned to further broaden the utility of nsearch.