2554 days ago
BBTools for bioinformatician !
...red" to keep output reads in the same order as input reads Finding reads with a...mbol gets replaced by the barcode; in both the input and output names, the "#" sym...can also give a custom prefix if you want. The input has to be text format, not .d...2294 days ago
3676 days ago
Barrnap: Bacterial ribosomal RNA predictor
...upports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and write GFF3 as output. It...2573 days ago
1664 days ago
Sample bandage input file for visual analysis
Sample bandage input file for visual analysis ...1239 days ago
Linux Sort Commands for Bioinformatics
...first column, then the second if the first is the same, and so on:sort input.txt sort a huge file (GNU sort ONLY):sort -S 1500M -t $HOME/tmp input.txt > sorted.txt sort sta...3650 days ago
A guide for complete R beginners :- Getting data into R
...lsquo;Monday’, ‘Tuesday’, ‘Wednesday’, ‘Thursday’, ‘Friday’); Usually however you want to input from a file. We have touched...3381 days ago
Most Commonly used Awk by Bioinformatician
...umn 3 is larger than column 5: awk '$3>$5' input.txt > output.txt extract column 2,4,5: awk '{print $2,$4,$5}' input.txt > output.txt awk 'BEG...NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt deal with simple CSV: a...3936 days ago
List of In-silico Binding Site Prediction Tools
...recognition servers, requiring only a 3D model and list of templates as inputs. A simple web interface is a...similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a...3767 days ago
3329 days ago
SPADes team announce new version SPADes v3.15
...;-New trusted contiguous use algorithm; -Switched to the memory allocator mimalloc; - PlasmidSPAdes and bgcSPAdes are now provided as an input assembly graph; - Import...1229 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matches the regex print it if it matches while($line = ){...2940 days ago
A multilayer perceptron (MLP) neural network in Perl
...#Tanh hidden neurons #Linear output neuron #To include an input bias create an #extra input in the training data #and se...atNum; my $errThisPat; my $outPred; my $RMSerror; my @trainInputs; my @trainOutput; # th...2939 days ago
Tryst with a Bioinformatician # Dr Altan Kara
...he field of bioinformatics (from any branch) must always be good about the environmental control. In other words, one should always easily control input output directories, modify fi...2385 days ago
Comment on "Short-read assembly using Spades !"
...the initial assembly is not satisfactory, SPAdes allows for an iterative assembly approach where the output from the previous assembly is used as input for another round of assembly...439 days ago
Comment on "Short-read assembly using Spades !"
...official website (http://cab.spbu.ru/software/spades/). It is available for Linux, macOS, and Windows operating systems. Prepare the input data: The input data should be in FASTQ forma...444 days ago