The computational biology group has constructed a number of programs, databases and tools for the archiving, analysis and interpretation of biomedical information. The focus has been to develop tools that integrate and visualize various data for gene discovery, predict variations to enable a directed study of polymorphisms, and to cluster and mine the available biomedical literature for hidden knowledge, i.e. text mining. The goal is to develop computational tools that enable the biomedical researcher to accelerate there research. These tools run on our various servers, and some of them and/or their results can be accessed via the internet.
The Garner Lab has created many informatics software applications, with the most popular tools described below.
Biomedical eText Data Mining:
eTBLAST - a text similarity engine, which accepts a query and then compares it to a collection of other text, especially medline. A variety of post-processors analyze the "hits" to provide added value to the user. Applications include reference searches, novelty assessment and duplication ethics.
Deja vu- A database of highly similar citations identified by eTBLAST. The databse includes over 70,000 pairs of citations and notes from manual inspection of some full text article pairs.
ARGH - a comprehensive catalog of biomedical acronyms and abbreviations extracted from MedLine abstracts.
DNA Sequence Analysis Computational Tools and Databases:
HaloGen - A system for the rapid discovery and optimization of peptide based ligands, jointly under development with Lynntech.
Eremorph,- A gene centric web-accessible database that offers to users special DNA sequence annotation that is a combination of unique computations and measurements with certain publicly available annotation. Eremorph contains these annotations overlaid upon genomic slices to which RefSeq genes are aligned, thus providing these data for coding, intron, untranslated, and promoter regions.
PCR Now - A tool for designing Real-Time PCR primers. Supplement to PathoGene for RT-PCR primer design in organisms not featured in the PathoGene database.
MicrosatDB - A database of genotyped microsatellite loci from over 400 human samples sequenced by the 1000 Genomes Project.
Gene/Protein collection and array Computational Tools:
Nome della Proteina (GI to Locus Link Convertor)- A new protein indentification resolution database. This database provides easy conversion of protein GI Numbers to Locus Link IDs and vice ersa. GO terms, products, AfCS IDs and analyses , and official names and symbols are also provided.
Biomedical Communications Tools:
Majorizer - a tool that analyzes your personal interest statement to suggest matching undergraduate majors works by comparing your entry to the class descriptions to help identify which majors at Virginia Tech teach the most classes that match your interests.
SpinOut - "A researcher’s guide to corporate identity,” was developed to help researchers with potential spinout companies from university laboratories access information on effective practices for corporate identity design. On this site we present concepts and examples of each component for an effective corporate identity package.