Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared tes...############################ # Read sequence file 1 #####################...lite(\*FILE); # loop through each sequence in file 1 while(my $entry =...to count dinucleotides, loop through sequence,...439 days ago
Download lumpy skin disease data !
Location https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=880745 The raw genome sequence data from the 2022 outbreak in India is available in the SRA Project PRJNA880745438 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems; my $total-bases = $sequence.chars; return $gc-count / $total-bases * 100; }...GCGCGCGCGC"; my $gc_content = calculate-gc-content($dna_sequence)...139 days ago
Raku script to find SSRs in fastq file !
sub find-ssrs(Str $sequence) { my @ssrs; for 2..$sequence.chars -> $min-repeats { for $sequence.chars...$min-repeats -> $max-...peats + 1; if $sequence.substr($max-repeat).index($re...-length, sequence => $repeat }...139 days ago
Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) = @_; $sequence = uc($sequence); # Convert the sequence to uppercase my $gc_count = () = $sequence =~ /[GC]/g; my $total_ba..._content; } # Example usage: my $dna_sequence...124 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
def multi_to_single_line_fasta(input_filename, output_filename): try:...utput_file: current_sequence = "" for lin...If a header line, write the previous sequence and then the new header...n') current_sequence...123 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
#!/usr/bin/perl use strict; use warnings; sub multi_to_single_line_f...t_filename': $!"; my $current_sequence = ""; while (my $line...If a header line, write the previous sequence and then the new header...rrent sequence $current_sequence...123 days ago
122 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gf...122 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $inp...ta, -format => 'fasta'); my $sequence = $seqio->next_seq; # Step...slated_seq = translate_frame($sequence, $frame); my $frame_type...122 days ago