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Here you will find links to other websites regarding epigenetic and tools useful in your research field.
CpG Islands

CpG island searcher
This software screens for CpG islands which meet the criteria selected in submitted DNA sequences (D. Tatai and S. Catherall)

CpGplot
This software screens for CpG islands which meet the criteria selected in submitted DNA sequences (EMBL-EBI).

Methylator
This software predicts whether CpG in a DNA sequence are likely to be methylated or not (M.K. Bashin et al.)

Primer design

MethPrimer
This programme is an online tool for designing bisulfite-conversion-based Methylation PCR Primers. It can design primers for Methylation-Specific PCR (MSP) and Bisulfite-Sequencing PCR or Bisulfite-Restriction PCR. The input sequence is DNA sequence in any format. The program returns results in both text and graphic view (Long-Cheng Li).

MethPrimerDB
A public database holding PCR primers for popular DNA methylation analysis methods (Methylation-specific PCR, Bisulfite-PCR-SSCP, Methylation-sensitive single-nucleotide primer extension, Combined bisulfite restriction analysis, Bisulfite sequencing) to prevent time-consuming primer design and experimental optimisation (Gent University).

Primer3
Picks (normal) PCR primers from a DNA sequence (S. Rozen and H.J. Skaletsky)

Gene seqences

GenBank
The NIH genetic sequence database.

Blast human sequences
Finds regions of similarity between human sequences.

Blast 2 sequences
This tool produces the alignment of two given sequences (Tatusova and Madden 1999).

Ensembl
Genome browser (EMBL-EBI, Sanger Inst.) - This site provides free access to all the data and software from the Ensembl project.

COBRA

Snake-Charmer
A tool for the selection of restriction enzymes for COmbined Bisulfite Restriction Assay (COBRA) (C. Grunau).

Bisulfide sequencing

MethTools
A toolbox to visualize and analyze DNA methylation data (analysis of bisulfite treated DNA). The software does the comparison between unconverted mother sequences and deaminated sequences, generates graphical outputs of methylation patterns and methylation density, estimates the systematic error of the experiment and searches for conserved methylated nucleotide-patterns. The software can be used to generate files suitable for the submission to MethPrimerDB (C. Gunau et al.).

BIQ_Analyzer
An excellent software tool for easy visualization and quality control of DNA methylation data from bisulphite sequencing (C. Bock).

siRNA design

siRNA Target Finder
Paste your mRNA sequence into the window, choose your preferred end structure (3' TT or UU), and the program will scan your sequence for AA dinucleotides. A report is generated indicating the position of the AA dinucleotide, the 21 base target and the corresponding sense and antisense siRNA oligonucleotides (Applied Biosystems).

DEQOR
A web-based tool for the design and quality control of siRNAs (Henschel et al. 2004).

siDirect
A web-based online software system for computing highly effective small interfering RNA (siRNA) sequences with maximum target-specificity for mammalian RNA interference (RNAi).

siRNA at Whitehead
This online tool helps you select oligos to knock down your gene of interest. After entering your sequence, choosing a pattern for your oligo nucleotides, and selecting various filter methods, you will be presented with a list of oligos matching your pattern. From this list, select those oligos you would like to consider further, based on their position within your sequence, the snps, and other criteria. Your results will be available directly on the web and/or will be emailed to you when they are ready. Needs registration which is free (Whitehead Institute for Biomedical Research).

siRNA Target Finder
Find siRNA target. Acceptable input are accession number and sequence. Five databases including human, mouse, rat and drosophila are available for blasting (GenScript).

TROD: T7 RNAi Oligo Designer
a web application that facilitates the design of DNA oligonucleotides for the synthesis of short interfering RNAs (siRNAs) with T7 RNA polymerase. It takes a cDNA sequence as input and automatically generates the appropriate DNA oligos for ordering. The output is organized so as to make it easy for the user to choose appropriate target sequences.

MicroRNA Target Scan

miRBase Target Database
Searchable database of miR targets on 3' UTR of genes in almost all genomes. Search can be done using miR id, gene name, EnsEMBL id, and keywords. But it does not accept user sequence input (Sanger Institute).

RegRNA
RegRNA is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. For microRNA target prediction, users can input a gene id or name, or a mRNA sequence, the program will scan the input sequence for targets of internally stored human microRNAs. Results are returned in table and graphic view (Department of Biological Science and Technology, National Chiao Tung University, Taiwan).

miRTar
miRTar is a web server which provides an intuitive interface to allow user input any miRNA/siRNA sequence for identifying miRNA targets against the 3'-UTR of mRNA of mammalian genes (BidLab, Institute of Bioinformatics, National Chiao Tung University , Taiwan).

Pic Tar
PicTar is an algorithm for the identification of microRNA targets. This online tool provides search function for microRNA targets on mRNA. Search can be done by microRNA or gene name.

RNA22 microRNA target detection
Given a microRNA and a mRNA sequence, the program returns microRNA targets on the sequence. A downloadable utility that allows you to install on your local computer and run batch queries (i.e. many microRNAs against many candidate target sequences). It is easy to install, set up and use. It also provides precomputed predictions for several organisms for downloading (IBM).

RNAhybrid
RNAhybrid is a tool for finding the minimum free energy hybridisation of a long and a short RNA. The hybridisation is performed in a kind of domain mode, ie. the short sequence is hybridised to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction (University Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research).

Resources

DNA methylation in cancer
Resource for scientists interested in the field of CpG island methylation as an epigenetic mechanism contributing to the processes of aging and age-dependent processes such as cancer development (Unversity of Texas).

Epigenetics
The official journal of the DNA Methylation Society.

Epigenetics News
Written and published by T. Covert, a student at Washington State University.

Epigenetics: A Web Tour (Science)
Collection of links to interesting Web resources on chromatin, methylation, imprinting, and a variety of other topics with an epigenetics bend. Also, a selection some groundbreaking research papers, Reviews, and Perspectives published in Science over the past five years, in a special new epigenetics section of the Functional Genomics Research Archive of this Journal.

Epigenome NeE I
Website of the european epigenetics research community (FP6 EU Grant), with news, protocols and links.

Epigenome NoE II
Epigenome NoE multilingual public science website.

Protocol online
A lab reference book, interesting for the numerous protocoles.

PubMed (NIH)
PubMed is a service of the U.S. National Library of Medicine that includes over 17 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. PubMed includes links to full text articles and other related resources.

Forum

BioForum
Discussion forum of www.protocol-online.org