BlastXtract2: Improving early exploration of (meta) genomes.

Heleen De Weerd,Microbiology And Systems Biology, Tno, Zeist, The Netherlands ,Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands ,Marcus J Claesson,Bernd Veen,

doi:10.6026/97320630011173

Heleen De Weerd, Microbiology And Systems Biology, Tno, Zeist, The Netherlands + Show 4 more

Open Access

https://doi.org/10.6026/97320630011173

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Abstract

To manage and intelligently mine the avalanche of genomic sequences intuitive and user-friendly graphical interfaces are required. Here we present BlastXtract2 which exclusively facilitates early exploration of un-annotated genomic and metagenomic sequences. Various formats of translated searches, including the commonly used BlastX, of multiple sequences against multiple protein databases can be uploaded to a relational database server, which can be accessed via a locally installed web-server. There, an intuitive GUI allows straightforward data-mining and enables quick detection of potential frameshifts and poorly sequenced or assembled regions, thereby contributing in making BlastXtract2 a unique and valuable tool for early exploration of (meta)genomic sequences.AvailabilitySource code, documentation and an online demo version are available at https://github.com/ ClaessonLab/BlastXtract2

Highlights

The development of user-friendly data-mining applications have for long been trailing the ever-increasing rate of genomic data generation
Translated searches (e.g. BlastX) of such multiple genomic sequences against protein databases are highly valuable for the early exploration of encoded functions
To meet these challenges we developed BlastXtract2, which is a substantial improvement over its first version [2]

Summary

Background

The development of user-friendly data-mining applications have for long been trailing the ever-increasing rate of genomic data generation. Translated searches normally precede and often complement gene prediction and annotation, which in turn require careful manual curation. Such search results can often reveal regions of poorer quality of sequencing and/or assembly through detection of frame shifts. To meet these challenges we developed BlastXtract, which is a substantial improvement over its first version [2]. Methodology: BlastXtract was written in Perl with CGI, DBI and BioPerl Graphics modules installed It runs on a Linux-based server and has been successfully tested on Ubuntu, Debian and Fedora. The functionality and improvements over its previous version are further described in the Implementation section below

BIOINFORMATION open access

Conclusion and future development