Results for "Sequence"
Bio-Scripts
Run Pango on your multifasta file !
...F_DATA/FASTA/Input_for_Cova_all_samples_combined.fa ** Running sequence QC ** Number of sequences detected: 320 Total passing...nability-limitations warnings.warn( processing block of 293 sequences 11/30/2021, 13:10:08 /home/...892 days ago
bash script to extract sequence by ids !
...e a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input:...s.txt ids_gene_ids.tsv | cut -f1 > ids.selected.txt # Extract fasta sequence that correspond to desired ge...828 days ago
Script to rapid genome clustering based on pairwise ANI
...ext, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt...Next, calculate pairwise ANI by combining local alignments between sequence pairs: anicalc.py -i -o...640 days ago
Perl script to find inverted repeats !
...n/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO->new(...430 days ago
Raku script to find palindrome in genomes !
...lindrome found at position $pos: $substring"; } } } } # Example usage my $dna = "GGATCCATGGCCTAGG"; # example DNA sequence find-palindromes($dna, 3, 8)...429 days ago
Perl script for chi-squared test !
...##################################### # Read sequence file 1 #####################...= new FAlite(\*FILE); # loop through each sequence in file 1 while(my $entry =...eq); # to count dinucleotides, loop through sequence, take 2 bp and increment the...416 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 PRJNA880745415 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 * 1...CGC"; my $gc_content = calculate-gc-content($dna_sequence); say "DNA Sequence: $dna_...116 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...ssr, End: $ssr, Length: $ssr, Sequence: $ssr"; }...116 days ago
Perl script to calculate GC content !
...l sub calculate_gc_content { my ($sequence) = @_; $sequence = uc($sequence); # Convert t...ce to uppercase my $gc_count = () = $sequence =~ /[GC]/g; my $total_ba..._content; } # Example usage: my $dna_sequence = "ATGCGCTAAAGCGAGCGAAGCGCTAG...101 days ago
