Results for "PSI Blast"
Bio-Scripts
Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation conda install -c bioconda blast #Windows installation Fir...wnload ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi...stead http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi...1130 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai...c License. # This script will parse a NCBI blastx output file and output the top N hits of each blast search result. # For each hi...Hits,$outfile) = @ARGV; print "Parsing the BLAST result ..."; my $in = Bio::S...2898 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1...GCGCACAGACAGATAAAAATTACAGAGTAC # generate the blast database $ makeblastdb -dbtype nucl -out EC -in EC...TAACCAATATAGGCATAGCGCACAGAC .... # query the blast database by id and coordinate...2836 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your...itendra Narayan #USAGE: ./selfBlast.sh extract #USAGE: ./selfBl...-f $MYDB.nhr ] then echo "BLAST database for MergedContigs.fa...o "You want entire sequence to blast" SEQ=$FASTAFILE else e...2636 days ago
Fill up the form and blast with perl
...'GCCCGCGGTCTCAGAGATCTCGATATATTATA'; $mech->get('http://www.arabidopsis.org/Blast/'); $mech->submit_form( form_name => 'myForm', fields => { 'Algorithm' => 'blastx', 'BlastTargetSet' => '...2309 days ago
Installing Busco version 4.0.6
...0 2.6 MB conda-forge blast-2.2.31 |...199 KB conda-forge r-ellipsis-0.3.0 | r36hcdc...::biopython-1.76-py37h516909a_0 blast bioconda/linux-6...gest-0.6.25-r36h0357c0b_2 r-ellipsis conda-forge/linux-64::...1436 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail ---------------------------------------------...libXt/1.1.5-foss-2016a BLAST+/2.3.0-foss-2016a-Python-2.7....2018 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Do...Ubuntu / Debian sudo apt-get install ncbi-blast+ CentOS # download latest...tp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.8.1+-x64...
1745 days ago
- (JitMetaENV) ➜ day2 conda install -c bioconda kraken2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solv...
1199 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bio...depends on the following software #BLAST #MCL #MUSCLE/MAFFT/PRANK #...aster) conda create -n wgd python=3.7 blast mcl muscle mafft prank paml...Commands: dmd All-vs.-all diamond blastp + MCL clustering. kde Fi...1187 days ago
