An easy to use web server for identifying regulatory RNA motifs and functional sites. Through its integrated user-friendly interface, user is capable of using various analytical approaches and observing results with graphical visualization conveniently.
Predicts iron-responsive elements in RNA or DNA sequences based on a sequence searcher Perl program. The SIREs web server uses a simple data input interface and provides structure analysis, predicted RNA folds, folding energy data and an overall quality flag based on properties of well characterized IREs. Results are reported in a tabular format and as a schematic visual representation that highlights important features of the IRE.
Connects motif content of the regulatory sequences with the logarithm of expression fold changes of a set of genes. miReduce is able to correlate the motif content of the 3'UTRs with the genome wide mRNA log fold changes in experiments involving of one or more miRNAs.
Estimates the concentration of gene expression codes in different non-coding parts of genes and transcripts, such as introns and untranslated regions. Chimera can be used for detecting and understanding gene expression codes in different parts of the genome/genes in previously un-studied organisms. The algorithm can be used for developing novel gene expression models and for gene expression engineering and synthetic biology systems.
Identifies conserved cis-elements in multiple sequence alignment of diverged coding sequences. cRegions is a program dedicated to detect a wide variety of functional elements in DNA and RNA viruses. It aims to study regions within diverged protein-coding sequences where the distribution of observed nucleotides is different from the expected distribution which is based on the amino acid composition and codon usage.
Predicts gene expression levels based on transcription factor (TF) binding alterations inferred from cis-regulatory variants. TF2Exp is able to evaluate the impact of single nucleotide polymorphism (SNPs) in linkage disequilibrium (LD) and uncommon variants, and can determine the alteration of gene expression for over three thousand genes. It can infer regulatory regions and TF binding events of each gene based on the reference cell line.
Predicts gene expression and adapts coding sequence of a target gene to any host organism. ChimeraUGEM is a program for model-free analysis and engineering of gene expression that includes implementations of several Chimera algorithms, as well as the codon adaptation index (CAI) model. It can be applied to organisms where gene expression measurements and models are missing, given a set of coding sequences.