Results for "genome letters"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import...1127 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -quer...1092 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse...1092 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Util qw/ shuffle /; my...while (my $line = ) { next unless $line =~ /^([ATGCN]+)/; my $genome = $1; my $len_genome...2906 days ago
- #!/usr/bin/env perl use strict; use warnings; use LWP::Simple; use XML::XPath; u...ure out URL for the DAS server. Example: # http://genome.ucsc.edu/cgi-bin/das/calJac3/...gment=chr14:482280,483280 my $URL_gene ="http://genome....
2901 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt...e will use values read from BLOSUM50) my $MATCH = 1; # +1 for letters that match my $MISMATCH = -1; # -1 for letters that mismatch my $GAP =...2896 days ago
Count GC Content in nucleotide sequence with Perl
#!/usr/bin/perl -w ### Usage: get_gc_content.pl...et_gc_content.pl } sub process_it { @letters = split(//, $seq); $gcco...$gcount = 0; $ccount = 0; foreach $i (@letters) { if (lc($i) =~ /[a-z]/) {...2896 days ago
Perl script to generate a random psuedo DNA sequence !
#!/usr/bin/perl print "Enter a number of nucleotides: \n"; chomp ($N = ); @b=qw/A T G C/;print ">Genome\n";while($l2874 days ago
Blast script to index and extract sequence !!
# look at the file $ head EC4115.fa >NC_011353.1 Escherichia coli O157:H7 str. EC4115 chromosome, complete genome. AGCTTTTCATTCTGACTGCAACGGGCA...7:H7 str. EC4115 chromosome, complete genome AGCTTTTCATTCTGACTGCAACGGGCAA...7:H7 str. EC4115 chromosome, complete genome...2843 days ago
Extract a range from genome file with perl.
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; my $in_file = $ARGV[0]; my $start_pos = $ARGV[1]; my $end_pos = $ARGV[2]; my $in = Bio::SeqIO->n...2618 days ago
