Results for "input"
Blogs
...e for a specific taxon based on sequence homologs in other species. The input is a multiple sequence alignm...data, and can also obtain an estimation of ancestral genomes, given an input tree. MLGO takes the advantag...2539 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...2280 days ago
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Bookmarks
- ...mance of three statistically-based variant detection tools:* SAMtools: Mpileup* GATK: Unified Genotyper* FreeBayesEach of these tools takes as its input a BAM file of aligned reads a...
3662 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...2559 days ago
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Files
- perl script analyzing codon usage in an input sequence to evaluate how efficiently it will be expressed in Anopheles gambiae. The input codon usage table derived from highly‐expressed A. gambiae genes is appended below.
1650 days ago
Sample bandage input file for visual analysis
Sample bandage input file for visual analysis ...1224 days ago
Pages
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...3636 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...3367 days ago
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Top-level pages
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...3921 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...3753 days ago
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Wire posts
News
- ...he Summary group duplicate less. (PR#15798) (Unix-alikes.) system(cmd, input = ) now uses ‘shell-exe...ge titles. The matrix methods of cbind() and rbind() allow matrices as inputs which have 2^31 or more elem...
3314 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...1215 days ago
Bio-Scripts
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 = ){...2926 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...2925 days ago
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Tryst
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...2371 days ago
Tags
Sample bandage input file for visual analysis
Sample bandage input file for visual analysis ...Tags: bandage, assembly, genome, visual, analysis, file, input
1224 days ago
Comments
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...425 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...430 days ago
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