Research in the Graveley lab is primarily focused on the regulation of alternative splicing and small RNA mediated gene regulation. These are fascinating and extraordinarily important mechanisms by which genes can be regulated. Our long-term goals...
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...
Ph.D. student in Computational Systems Biology
Location : The Luxembourg Centre for Systems Biomedicine (LCSB) at the University of Luxembourg, Luxembourg, Luxembourg
Deadline for applications : unknown.
Description :
The Luxembourg Centre...
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...
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...
The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher...
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...
physicsdatabase.com - Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.
Please add ur links/bookmarks in comment section.
➜ bin git:(master) ✗ ls -l
total 68
drwxrwxr-x 3 urbe urbe 4096 Jun 15 12:15 lib
-rwxrwxrwx 1 urbe urbe 65141 Jun 15 17:13 LINKS
➜ bin git:(master) ✗ pwd
/home/urbe/Tools/LINKS_1.8.6/bin
➜ bloomfilter git:(master) ✗ swig -Wall -c++...