Bioinformatics

Overview

SIMO investigators have developed several novel bioinformatics approaches and software tools in the course of conducting their research. The following tools are available for general use by the scientific community.

Tools for BLASTn

» Online BLASTn tool for single sequences - Web application for blasting a user-contributed 16S sequence against the SIMO database using the NCBI BLASTn program. This tool returns results in HTML format, with hyperlinks to SIMO sequence detail pages and an augmented alignment summary table listing nucelotide identity calculations.

» Library BLASTn tool for multiple sequences - Web application for blasting an entire Fasta-formatted 16S library against the SIMO database. Each sequence is blasted independently, and an overall summary index page is created for navigating to individual alignment pages (sample output). This tool uses a distributed computing architecture to control load on the server. (Note: registration required)

Tools for Automated Bacterial Classification

» RDPquery - Java application for generating taxonomic identifications for 16S rRNA prokaryotic gene sequences. The program utilizes The Ribosomal Database Project's Sequence Match tool to retrieve classification information for similar type sequences, then performs local pairwise Smith-Waterman alignments and assigns unknown sequences to taxonomic ranks based on similarity-weighted cut-off limits.

» RDP Agent - MATLAB toolbox containing programs for automatic bacterial classification based on RDP taxonomy and local Smith-Waterman sequence alignment, batch sequence alignments, and taxonomic coverage summarization of sequence libraries (source code not yet available online - contact the SIMO database administrator for information).

» SIMO Online Analysis Tools - Web-based version of SIMO's bacterial classification tools, supporting analysis of 16S rRNA gene sequence libraries plus generation of Fasta files with environmental metadata formatted for batch submission to GenBank using the NCBI Sequin program. This tool uses a distributed computing architecture to control load on the server. (Note: registration required)

Tools for Statistical Comparison of 16S rRNA Sequence Libraries

» LIBSHUFF Program - Perl program for comparing two libraries of 16S rRNA gene sequences to determine if they are significantly different.

» webLIBSHUFF - Web-based implementation of LIBSHUFF

Other Bioinformatics Tools

» User-contributed tools and web links (Note: registration required)