Results for "PSI Blast"
Bio-Scripts
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; u...y_DB/' ); #Install diamondDB __END__ # BlastDB download my $result = `mkd...print "Download started"; } if [ ! -d "$PWD/blastDB" ]; then if [ ! -d "$P...1157 days ago
- blastpgp arguments: -d Database [String] default =...ties and blunt ends, 7 = XML Blast output, 8 = Tabular output...stdout -y Dropoff (X) for blast...= 250 -C Output File for PSI-BLAST Checkpointing [File Out] Optional -R Input File for PSI-BLAST Restart [File In] Option...
947 days ago
Command line to create blast uniref database !
#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program. The 'blastpgp' program is...FTP site: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.26/....-i uniref90filt #When using NCBI BLAST+ the 'formatdb' command shoul...947 days ago
Command line to download blast database / protein
#download all available nr - protein database as...ses are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / de...to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #cat them...940 days ago
Download desire version of Blast software !
#Create a directory and wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-...#unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #S...NUM_THREADS=??? module load ncbi-blast/2.6.0_x86_64939 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options...Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT...Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB...939 days ago
Installing Covid19 Environment !
(base) vikas@vikas-Lenovo-ideapad-320-15ISK:~/vinodLab/Genepi$ conda env create -f...###################################################################### | 100% blast-2.12.0 | 22.4 MB |...920 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...he search at the cost of sensitivity: blastn -query -db -outfmt '6 std...632 days ago
- (jitENV) [jnarayan@hn1 preetiDATA]$ blastn -task blastn -query list_flank_0.fa -subject ../monkeypoxDATA_07_06_22/JIT_gisaid_pox_2022_09_06_07.fasta -evalue 20000000 -word_size 5 -num_threads 4 -outfmt 6 -out blastn_0.txt -qcov_hsp_perc 100 -perc_identity 100 -max_target_seqs 10000
589 days ago
Perl script to parse blast results and plot basic stats !
...qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./p...last_file = shift @ARGV; my @blast_entries = parse_blast($blast_...dentity = calculate_average(\@blast_entries, 'PERCENT_IDENTITY');...avg_bitscore\n"; sub parse_blast { my ($file) = @_;...91 days ago
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