Abstract
BackgroundThe NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST into Galaxy was a natural step for sequence comparison workflows.FindingsThe command line NCBI BLAST+ tool suite was wrapped for use within Galaxy. Appropriate datatypes were defined as needed. The integration of the BLAST+ tool suite into Galaxy has the goal of making common BLAST tasks easy and advanced tasks possible.ConclusionsThis project is an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several examples of applications are described here.
Highlights
The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses
The NCBI BLAST web interface is designed for performing one query at a time, which means that larger searches have to be automated for batch processing within a script or by running BLAST as a command line program
Automation became increasingly important for the analysis of BLAST output as these datasets have grown larger
Summary
The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale pan-genome analyses. This article describes our NCBI BLAST+ [16] wrappers for Galaxy and associated tools and datatype definitions. Each row lists a separate Galaxy tool, all available from https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/ on the Galaxy Tool Shed [9].
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