Results for "BLAST databases"
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...Download ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi...instead http://ftp.ncbi.nlm.nih.gov/blast/exe...1160 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed...License. # This script will parse a NCBI blastx output file and output the top N hits of each blast search result. # For each hi...its,$outfile) = @ARGV; print "Parsing the BLAST res...2927 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. E...CGCACAGACAGATAAAAATTACAGAGTAC # generate the blast database $ makeblastdb -dbtype nucl -out EC -in EC...AACCAATATAGGCATAGCGCACAGAC .... # query the blast dat...2865 days ago
- #!/usr/local/bin/perl -w # NOTE: YOU MUST CHANGE THE LI...space available. Databases size scales linearly...ence length. With default parameters,databases are are roughly...
2706 days ago
BASH script for SelfBLAST a genome
#!/bin/bash #self BLAST a genome -- Expecting you have blast and samtools installed in your sy...: Jitendra Narayan #USAGE: ./selfBlast.sh extract #USAGE: ./selfBl...f [ -f $MYDB.nhr ] then echo "BLAST database for MergedContigs.fa...echo "You want entire sequence to blast"...2665 days ago
Fill up the form and blast with perl
use WWW::Mechanize; use strict; use warnings; my $mech = WWW::Mechanize->new; my...ATTATA'; $mech->get('http://www.arabidopsis.org/Blast/'); $mech->submit_form( f...e => 'myForm', fields => { 'Algorithm' => 'blastx',...2338 days ago
Installing Busco version 4.0.6
(base) jit@jit-HP-Pro-3335-MT: conda install -c bioconda -c conda-forge busco=4.0.6 C...py37h516909a_0 2.6 MB conda-forge blast-2.2.31 |...a-forge/linux-64::biopython-1.76-py37h516909a_0 blast...1466 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/...libXt/1.1.5-foss-2016a BLAST+/2....2047 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Downloa...Ubuntu / Debian sudo apt-get install ncbi-blast+ CentOS # download latest...get ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LA...
1775 days ago
- (JitMetaENV) ➜ day2 conda install -c bioconda kraken2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve....
1228 days ago
