XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data Export

@article{citeulike:3384601, abstract = {BACKGROUND: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, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. 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; [<a href="\#B1">1-3</a>]) 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 or amplicons, with sequences and other data stored in a single file.CONCLUSION:XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.}, author = {Frank, Daniel}, citeulike-article-id = {3384601}, citeulike-linkout-0 = {http://dx.doi.org/10.1186/1471-2105-9-420}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18840282}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18840282}, day = {07}, doi = {10.1186/1471-2105-9-420}, issn = {1471-2105}, journal = {BMC Bioinformatics}, month = {October}, number = {1}, pages = {420+}, posted-at = {2009-10-21 16:00:37}, priority = {2}, title = {XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data}, url = {http://dx.doi.org/10.1186/1471-2105-9-420}, volume = {9}, year = {2008} }

TY - JOUR ID - citeulike:3384601 L3 - citeulike-article-id:3384601 N2 - BACKGROUND: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, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. 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; [<a href="#B1">1-3</a>]) 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 or amplicons, with sequences and other data stored in a single file.CONCLUSION:XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware. IS - 1 JF - BMC Bioinformatics SN - 1471-2105 TI - XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data VL - 9 SP - 420 AU - Frank, Daniel PY - 2008/10/07/ UR - http://dx.doi.org/10.1186/1471-2105-9-420 ER -