XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects.
Results: XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for high-throughput analysis of environmental rRNA gene sequences, but can be used for any sequencing project.
XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats.
Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones, with sequences and other data stored in a single file.
Conclusions: XplorSeq will benefit researchers who are engaged in analyses of environmental sequence data. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to any sequencing project.
The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.
Author: Daniel N Frank
Credits/Source: BMC Bioinformatics 2008, 9:420
Published on: 2008-10-07
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