Ligand Docking Tools and Software !
Ligand docking referred to cases where small molecule (“ligand”) is being docked into much larger macromolecule ("target"). The following is partial list...2215 days ago
Tools for Protein-Protein Docking !
Predicting the structure of protein–protein complexes using docking approaches is a difficult problem whose major challenges include identifying correct solutio...2215 days ago
2203 days ago
Creating conda environment for python2.7
...e command. For details, run conda create --help. ➜ redundans git:(master) ✗ conda cre...# To deactivate an active environment, use:# > source deactivate# ➜ redundans git:(master) ✗ source ac...2202 days ago
Learning Python Programming - a bioinformatician perspective !
...a of big biological data, python and biopython is getting more popularity due to its easy-to-use features...characters (for example, strings of DNA bases and protein amino acid residues, which we as biologists are...2195 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
...20s13 r1.fq r2.fq stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap2194 days ago
Gap filling or Contigs extensions tools !
...eRisi lab. Its meant to do something very similar. http://derisilab.ucsf.edu/index.php?page=software Yo...oinformatics-solutions/sspacev12/), ATLAS tools (http://www.hgsc.bcm.tmc.edu/content/bcm-hgsc-software), a...2178 days ago
My commonly used commands in Bioinformatics
FYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | ra...2123 days ago
List of non-commercial NGS genotype-calling software
...sequencing (NGS) data, which are produced extensively by genetics an...ysis, which includes a single individual genotype caller (SOAPsnp)...genotype calling using single individuals and allele frequencies. Si...ita) MaCH http://genome.sph.umich.edu/wiki/Thunder Multi-sample LD...2109 days ago
Parallel Processing with Perl !
...to use fork in your code, that’s okie too..There are many useful modules which do it for you very efficiently. One really useful module is Parallel::ForkManager. Y...2092 days ago