Tools for Protein-Protein Docking !
...g and clustering. Refinement of interface side-chains 3D-Garden Global rigid se...tarity and Lennard–Jones potential Side chain and backbone dihedral refine...of conformations. Refinement of interface side-chains and re-scoring MolFit ...2216 days ago
2204 days ago
Creating conda environment for python2.7
...p;flag: conda create --no-default-packages -n myenv python TIP: You can add much more to the conda create command. For details, run conda create...2203 days ago
Learning Python Programming - a bioinformatician perspective !
...and 3 are quite different. This tutorial uses Python 3, because it more semantically correct and supports newer features. I will post tutorial on daily basis on this page. Check t...2196 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ && bwa sampe hs37m r1.sai r2.sai r1.f...2195 days ago
Ancestral sequence reconstruction steps !
...ps? 1- Alignments "Mafft - http://mafft.cbrc.jp/alignment/software/source.html" mafft --maxiterate 1000 --reorder --thread 24 --genafpair Dataset.fasta > Dataset_A...2192 days ago
Gap filling or Contigs extensions tools !
...e novo assembly approach to fill the gap within paired reads" or "Toward almost c...terest, and the set S of reads those contigs contain. Let C = C0. 2. Repeat:...hin, or extending, contigs in C. b. Identify unpaired reads that align extending...2178 days ago
LINKS scaffolder bloomfilter setting !
...quired) -s file-of-filenames, full path to long sequence reads or MPET pairs [see below] (Multi-FASTA/fa...OT USING MPET. WHEN SET, LINKS WILL EXPECT A SPECIAL FORMAT UNDER -s ! Paired MPET reads in their origin...2164 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output f...2152 days ago
Interview Puzzles for Bioinformatician !
...zzle Six pirates and Gold Coin puzzle Probability of having boy Random Airplane Seats Inverted playing...m Number of Weigths One Bulb with 3 Switches Find the minimum number of aircraft Burning ropes to measu...2133 days ago