Converting BLAST output into CSV
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something....2352 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\="\n"'perl -pe 'BEGIN { $\="\n" }'perl -pe '$_ .= "\n"'perl -pe 's/$/\n/'perl -nE 'say' # Double space a file, e...2317 days ago
List of visualization tools for network biology
Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis...2303 days ago
Installing Bio::SCF perl module
Most Perl modules are written in Perl, some use XS (they are written in C) so require a C compiler (it's easy to get this setup - don't panic), see...2233 days ago
Protein-Protein Interaction Sites Predictions !
The study of Protein–Protein Interactions (PPIs) has a crucial role in biology, medicine and the pharmaceutical industry. PPIs can be investigated from two aspects: T...2217 days ago
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 of doc...2217 days ago
Creating conda environment for python2.7
TIP: By default, environments are installed into the envs directory in your conda directory. Run conda create --help for information on specif...2205 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within paired reads" or "Toward...2180 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.fast...2125 days ago
Tools for Geospatial data analysis !
Geospatial data is becoming increasingly important in many fields, including urban planning, environmental science, public health, and more. These tools...425 days ago