Category Cross-Omics>Next Generation Sequence Analysis/Tools

Abstract SeqBuster is a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets.

The high flexibility of this tool is illustrated by the multiple choices offered in the pre-analysis for mapping purposes and in the different analysis modules for data manipulation.

To overcome the storage capacity limitations of the web-based tool, SeqBuster offers a stand-alone version that permits the annotation against any custom database.

SeqBuster integrates multiple analyses modules in a unique platform and constitutes one of the first bioinformatic tools offering a deep characterization of miRNA variants (isomiRs).

The application of SeqBuster to small-RNA datasets of human embryonic stem cells revealed that most miRNAs present different types of isomiRs, some of them being associated to stem cell differentiation.

The exhaustive description of the isomiRs provided by SeqBuster could help to identify miRNA-variants that are relevant in physiological and pathological processes.

SeqBuster overview --

SeqBuster is a web-based bioinformatic tool offering a custom analysis of deep sequencing data at different levels, with special emphasis on the analysis of miRNA variants or isomiRs (as stated above...).

SeqBuster offers three (3) tools to analyze all your small RNA data coming from Illumina sequencing.

1) Installation - How to start using it.

2) JAVA visual interface version: seqbusterviz & Quick Start - seqbuster intenface and Quickdemo.

3) adapter removal: remove 3' adapter - adrec.

4) miraligner: miRNA annotation using miRBase database.

5) R package isomiRs to visualize isomiRs and miRNA abundances in a group of samples (new).

6) seqcluster - analyzes the rest of small RNAs and annotate to multiple databases in bed format (new).

Note: SeqBuster home page is now a Wiki page (see their documentation page and see below...).

SeqBuster Main Page (Wiki) content --

1) adrec - An adapter recognition and removal from reads tool.

2) Home

3) How to start using it.

4) isomiRs

5) miraligner - A mapping of reads to the miRBase database tool.

6) Quickdemo

7) seqbuster intenface

8) seqcluster - clustering of small RNA sequences.

SeqBuster Additional info --

For additional info on SeqBuster see the following paper:

Lorena Pantano, Xavier Estivill, Eulalia Marti; SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells; Nucl. Acids Res., Vol. 38, No. 5. (1 March 2010), e34.

System Requirements

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Manufacturer Web Site SeqBuster

Price Contact manufacturer.

G6G Abstract Number 20787

G6G Manufacturer Number 104361