Our soft.

if ((light eq dark) && (dark eq light)
&& ($blaze_of_night{moon} == black_hole)
&& ($ravens_wing{bright} == $tin{bright})){
my $love = $you = $sin{darkness} + 1;
};

Angie Winterbottom

Riboseq.Org

GWIPS-viz is a genome browser for visulization of ribo-seq data. The broswer is at the early stage of development.

RiboGalaxy is an instance of Galaxy tailored for ribosome profiling analysis.

Databases

DARNED is a DAtabase of RNa EDiting in humans. Publically available data on RNA editing are collected in DARNED and mapped to the reference human genome. Each entry in DARNED can be explored in the context of Genome Browsers (UCSC and ENSEMBL).

Recode-2 databases is a compilation of information on genes that utilize recoding during their expression.

Computer tools

RUST is a software for normalization of ribosome profiling data. It determines global factors influencing distribution of ribosome footprints across the transcriptome. Thus RUST is able to predict experiemntal density of footprints with high accuracy. Among numerous applications it can be used for quick detection of sequencing biases in cDNA libraries. An implementation of RUST is also available through RiboGalaxy.

ARFA [ U_of_U mirror ] is a program for automatic annotation of bacterial class-I release factors (RF1, RF2 and RFH), ARFA recognizes sites of ribosomal frameshifting in RF2 encoding genes and annotate RF2 CDS properly (contrary to only partial CDS, which is the case in many published genomes).

OAF [ U of U mirror ] is a program for identification and annotation of antizyme CDS in EST sequences or mRNA sequences predicted from genomic sequences. OAF detects sites of +1 programmed ribosomal frameshifting required for antizyme synthesis.

Codonevo is a program for designing computer simulations of the triplet genetic code evolution.

CodonLogo is a Sequence Logo based tool for visualizing conserved patterns in multiple alignments.

viPVB (2007-2016)