The Human Genomic Melting Map

Liu F,, TÝstesen E, Sundet JK, Jenssen TK, Bock C, et al. (2007) PLoS Comput Biol. In Press.

(doi:10.1371/journal.pcbi.0030093.eor)


  

I.

Brief Introduction of the Human Genomic Melting Map Project

The human genomic melting map is a calculated representation of cooperativity in the human genome. This implies that it provides information with respect to the probability that a DNA bubble is formed, thus providing single stranded DNA to be accessible for cellular functions. The map was established in order to provide a resource for the community to explore its biological content further. Please contact Eivind Hovig for further inquiries regarding these matters. Presently, we only provide the human genome in its hg17 incarnation, i.e. the May 2004 version. We will update with the latest release, once calculation has been completed.

Background

The group has had a long standing interest in methods for mutation detection, and has published a significant body of papers on variations of denaturing gradient gel electrophoresis to this end. Presently, the methodology is developed for capillary electrophoresis using a cycling temperature system, for robust, cheap and fast assays using standard sequencing machines. This work has proven to us (and others) that prediction algorithms for DNA denaturation is well founded.

 

Source code

The source code (Fortran) is available upon request to Eivind Hovig, and is released under the GNU GPL license. It may be used to run chromosome length calculations. It is based on the MELT87 program, by Leonard S. Lerman, implementing the Poland-Fixman-Freire algorithm.

Online tool for calculating parameters of loop entropy parameter approximation


This tool is made available to derive a parameter set for the Poland algorithm approximation of loop entropy suitable for the length of the sequence under study.

 

Melting map data

We here provide the raw data of the melting map, for download and further use by others. The format is compressed plain text files (chr*.txt.bz2).

 

Human genomic melting map browser

This resource provides functionality for browsing the actual melting profile for a given sequence of the human DNA. The graphics are handled by SVG, thus a plugin may be required, depending on your browser. Most browsers now are able to handle SVG by default.

 

Ensembl combined browser

We have also made available a possibility to use the melting map data with the Ensembl browser as a DAS source. As the data do not represent the current version of the genome, it is necessary to follow the instructions provided to view the archived version of the genome with Ensembl.

 

Supplementary analytical results

We here provide the inputs for the analysis described in the paper, and output where relevant.