Blast script to index and extract sequence !!
...H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAA...AAAATTTTATTGACTTAGG TCACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAG...:H7 str. EC4115 chromosome, complete genome AGCTTTTCATTCTGACTGCAACGGGCAATATGT...2848 days ago
Perl script to insert sequence in contig !!
..., s = '$s' ) \n"; # OUTPUT: # s = ATATGATGATAGATGATAGTAGATAGATAGATAGATAGATAG # insert = 'CCCC ' # (now, s = ATATGATGATAGATGATAGTAGATAGCCCCATAGATAGATAGATAG' )";2705 days ago
Calculate ATGC percentage in parallel with perl
...$length=length $DNA; my $a=($DNA=~tr/A//); my $b=($DNA=~tr/C//); my $c=($DNA=~tr/G//); my $d=($DNA=~tr/T//); my $Total=$a+$b+$c+$d; my $GC=($DNA=~s/GC/GC/g); my $AT=($DNA=~s/AT/AT...2652 days ago
Download the genome from NCBI using bash script/command
...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|'...2528 days ago
Download the gff files from NCBI using bash script/command
...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCA_.+)|\1\2/\2_genomic.gff.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|'...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|'...2520 days ago
Clump Finding Problem Solved with Perl
...in Genome. use strict; use warnings; my %myHash; my $string="CGGACTCGACAGATGTGAAGAAATGTGAAGACTGAGTGAAGAGAAGAGGAAACACGACACGACATTGCGACATAATGTACGAATGTAATGTGCCTATGGC"; my $subStr="?"; my...2330 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/ur...2328 days ago
Fill up the form and blast with perl
use WWW::Mechanize; use strict; use warnings; my $mech = WWW::Mechanize->new; my $sequence = 'GCCCGCGGTCTCAGAGATCTCGATATATTATA'; $mech->get('http://www.arabidopsis.org/Blast/...2322 days ago
Create genome scaffolding with Perl
...$b); } sub rc { my ($seq) = @_; $seq =~ tr/ACGTUYRSWMKDVHBXN-/TGCAARYSWKMHBDVXN-/; # work on masked sequences as well $seq =~ tr/acgtuyrswmkdvhbxn/tgcaaryswkmhbdvxn/; return(sca...2305 days ago
Download genomes in batch from NCBI
curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/assembly_summary.txt' | awk '{FS="\t"} !/^#/ {print $20}' | sed -r 's|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/)(GCA/)([0-9]{3}/)([0-9]{3}/)([0-9]{3}/)(GCA_.+)|\1\2\3\4\5\6/\6_genomic.fna.gz|' > genomic_file2259 days ago