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EBWS: Essential Bioinformatics Web Services for Sequence Analyses.

Dimitrios Kaloudas, Nikolet Pavlova, Robert Penchovsky

IEEE/ACM Transactions on Computational Biology and Bioinformatics

|July 12, 2018

Summary

This summary is machine-generated.

Essential Bioinformatics Web Services (EBWS) offer a user-friendly PHP server with nine tools for DNA, RNA, and protein sequence analysis. These bioinformatics tools include sequence generation, pattern searching, and CRISPR-Cas9 guide RNA design.

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Area of Science:

Bioinformatics
Computational Biology
Molecular Biology

Background:

Bioinformatic analyses of DNA, RNA, and protein sequences are crucial in modern biological research.
Accessible and user-friendly web tools are needed to support these analyses for researchers.
Existing web services may have limitations in functionality or accessibility.

Purpose of the Study:

To develop and present a new suite of Essential Bioinformatics Web Services (EBWS) for sequence analysis.
To provide a user-friendly interface for various molecular biology tasks.
To offer a comprehensive set of tools for DNA, RNA, and protein sequence manipulation and analysis.

Main Methods:

Implementation of a new PHP-based web server hosting nine distinct web applets.
Development of tools for sequence generation (oligomers, mutations), pattern searching, and restriction enzyme digestion.
Integration of calculators for melting temperature (TM) and annealing temperature, along with a guide RNA (gRNA) generator for CRISPR/Cas9.

Main Results:

Nine functional web-based applets are available, covering a wide range of sequence analysis needs.
The pattern-searching tool supports complex queries with unlimited motif inputs using Regex.
The DNA restriction cutter uses an extensive database of 1502 enzymes, and the gRNA generator includes 25 bacterial genomes.
All tools are accessible online without restrictions at http://penchovsky.atwebpages.com/applications.php.

Conclusions:

The EBWS provide a valuable and accessible resource for researchers performing DNA, RNA, and protein sequence analyses.
The user-friendly interface and diverse functionalities enhance the efficiency of molecular biology research.
The comprehensive and unrestricted nature of these web services supports broad scientific discovery.