Results for "BLAST databases"
Bio-Scripts
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slig...depends on the following software #BLAST #MCL #MUSCLE/MAFFT/PRANK #...ster) conda create -n wgd python=3.7 blast mcl muscle mafft prank paml...Commands: dmd All-vs.-all diamond blastp +...1231 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...U = 'https://www.arb-silva.de/fileadmin/silva_databases/release_138_1/Exports/SIL...); #Install diamondDB __END__ # BlastDB download my $result = `mkd..."Download started"; } if [ ! -d "$PWD/blastDB" ]; then if [ ! -d "$PWD/b...1188 days ago
- blastpgp arguments: -d Database [String] default = nr -i...o identities and blunt ends, 7 = XML Blast output, 8 = Tabular output,...fault = stdout -y Dropoff (X) for blast extensions in bits (default i...ault = 250 -C Output File for PSI-BLAST Che...
978 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' prog...e: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/....ref90filt #When using NCBI BLAST+ the 'formatdb' command should be...978 days ago
Command line to download blast database / protein
...le file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / de...s to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #cat them into...971 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #S...rt OMP_NUM_THREADS=??? module load ncbi-blast/2.6...970 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name...https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB...outpath/swissprot: mmseqs databases UniProtKB/Swiss-Prot outpath/...ownloaded and prepared by the databases command. More information...970 days ago
Installing Covid19 Environment !
...#################################### | 100% blast-2.12.0 | 22.4 MB |...u still need to manually update the taxonomy databases before Krona can generate tax...The default location for storing taxonomic databases is /home/vikas/anaconda3/envs...951 days ago
- #Installing MySQL on Ubuntu #To install MySQL on your Ubuntu server follow the st..., recommended option is to create a new administrative user with access to all databases: mysql > GRANT ALL PRIVILE...
947 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std...up the search at the cost of sensitivity: blastn -q...663 days ago
