Results for "C"
Bio-Scripts
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO;...enome.fasta"; # read genome sequence my $seqio = Bio::SeqIO->new...ort->next_result()) { my $rm_match = $rm_result->repeat_consens...result->strand(); if ($rm_class eq "Inverted") {...488 days ago
Perl script to find edit distance between two sequences !
#!/usr/bin/perl use strict; use warnings; sub edit_distance { my ($s1, $s2) = @_; my $len1 = length($s1); my $len2 = length($s2); my @dp; for (my $i = 0; $i488 days ago
Raku script to find palindrome in genomes !
...tr $str) returns Bool { $str.=uc; # convert to uppercase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.fl...-> $length { for 0..^$dna.chars - $length -> $pos {...# Example usage my $dna = "GGATCCATGGCCTAGG"; # example DNA se...488 days ago
R script to covert and export html page to png
# Library library(streamgraph) # Create data: data481 days ago
- (base) [lege@hn1 testVisanu]$ conda create -n pythonENV python=3.10 scipy=1.13.0 astroid babel Channels: - conda-forge - bioconda - defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.
55 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared test of the dinucleotide frequencies of two FAS...a->nextEntry) { my $seq = uc($entry->seq); # to count di...hi squared value = %6.2f\n", $chi_total; print "Signif...474 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 PRJNA880745473 days ago
- #!/usr/bin/env Rscript library(RCircos) # usage: Rscript make_circos.r # parse args args = commandArgs(trailingOnly=TRUE) sv.file
362 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 / $total-bases * 100;..._content = calculate-gc-content($dna_sequence); say "DNA Sequence: $dna...175 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...+ 1; if $sequence.substr($max-repeat).index($r...nd: $ssr, Length: $ssr, Sequence: $ssr"; }...175 days ago
