Predicts protein sequences encoded in small viral genomes. VIGOR is a web-based genome annotation program for five different viral agents: influenza, rotavirus, rhinovirus, coronavirus and SARS coronavirus. The software can predict protein coding genes with for those 5 different RNA virus types and has the capability to assign function to the predicted open reading frames (ORF) and genotype influenza virus.
Enables same-day identification of colony isolates recovered from investigative food samples. GeneSippr is a whole-genome sequencing (WGS) approach for the analysis of single colony isolates based on the sampling (or ‘sipping’) of raw data during the early stages of the WGS process, to determine the presence of pre-defined gene markers and evaluate a set of quality metrics designed to validate the analysis.
Detects and corrects sample mix-ups with high sensitivity and specificity. MixupMapper measures the difference between actual gene expression levels and predicted expression levels that are solely based on genotype data of cis-single nucleotide polymorphisms (SNPs). It depends on an initial set of cis-expression quantitative trait loci (cis-eQTLs) that can be detected in the data. This tool is useful for genetical genomics datasets or genome-wide datasets.
Evaluates difficult to assess regions that uses Structural variation (SV) calls and map ability to generate a genome-wide score. DangerTrack is a package that contents: (i) generated DangerTrack scores, (ii) scripts to first prepare, clean, bin the data, then combines and summarizes binned data, and (iii) inputs from 1000 Genomes Project breakpoints and Genome in a Bottle breakpoints.
Collects and collates data from various databases such as KOME, INE, RED. Rice PIPELINE provides a scientific resource on rice and makes them readily available through the input of any clone sequence, clone name, GenBank accession number, or keyword. In the case of a sequence query, users can select the BLAST condition, the type of full-length cDNA information (nucleic acid, amino acid), indica and japonica genome information, and the microarray EST.
Performs summary Mendelian Randomisation (MR) and instrumental variable analysis. Mrrobust can help users to estimate causal effects and permits to correct or attenuate bias thank to the utilization of SIMEX or Bayesian error in variables regression methods. The performance of this tool was evaluated by performing two analyses investigating potential relationships between adiposity, height, and serum glucose.