In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.
mummer4.github.io - MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing...
Sandelin group have a deep interest in most biology, but focus on gene regulation and the many areas that are connected with this, including transcriptomics, epigenetics and technological and informatics aspects.
The group is both computational...
github.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
Using AlignGraph
AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...
Agricultural research in modern scientific arena is being represented by proper integration among various research fields of biological, chemical and physical sciences, because this field encompasses many more complexities of biology in nature. In...
crossmap.sourceforge.net - CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10 (GRCm38)).
It supports most commonly...
A post-doctoral fellowship is available in the research groups of Nick Goldman (EBI) and John Welch (Genetics Department, Cambridge University) under the EMBL-EBI / Cambridge Computational Biomedical Postdoctoral Fellowship scheme.
The project is...
http://assemblytics.com/ - Download and install MUMmer
Align your assembly to a reference genome using nucmer (from MUMmer package)
$ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT
Consult the MUMmer manual if you encounter problems
Optional: Gzip...
Mike Ritchie Lab primary research focus is the detection of susceptibility genes for common diseases such as cancer, diabetes, hypertension, and cardiovascular disease, among others. The approaches will involve the development and application of new...