Results for "blast"
Bio-Scripts
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
...t( to => 'third_party_DB/' ); #Install diamondDB __END__ # BlastDB download my $result = `mkd...$content"))) { print "Download started"; } if [ ! -d "$PWD/blastDB" ]; then if [ ! -d "$P...1153 days ago
- blastpgp arguments: -d Database [St...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 Checkpointing [File Out] Opt...
942 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#The NCBI BLAST+ distribution does not include 'blastpgp', it has been replaced by the 'psiblast' program.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...942 days ago
Command line to download blast database / protein
...where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi.nlm.nih.gov/blast/db/ # Database detail / de...#First run this to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #cat them...935 days ago
Download desire version of Blast software !
...nd wget it wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-....tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #S...ort OMP_NUM_THREADS=??? module load ncbi-blast/2.6.0_x86_64934 days ago
Downloading mmseqs databases !
...- NR Aminoacid - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - NT Nucleotide - https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA - PDB...934 days ago
Installing Covid19 Environment !
...######################################################################################################################################### | 100% blast-2.12.0 | 22.4 MB |...916 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...627 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
584 days ago
Perl script to parse blast results and plot basic stats !
...til qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./p...$blast_file = shift @ARGV; my @blast_entries = parse_blast($blast_...t_identity = calculate_average(\@blast_entries, 'PERCENT_IDENTITY');...$avg_bitscore\n"; sub parse_blast { my ($file) = @_;...86 days ago
- « Previous
- 1
- 2
- Next »
