Results for "Multiple Sequence Alignment Algorithms"
Bio-Scripts
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use meg...blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt...ext, calculate pairwise ANI by combining local alignments between sequence p...693 days ago
Identify genome-wide synteny with LASTZ alignment
#This is the walkstrough how to identifiy genome-wide synteny markers based on LASTZ alignment. Step1：Mask the repeat sequences for both genomes and chromosomes. RepeatMasker -pa...mall -lib custom.TE.lib_for_FF.fa FFChr1.txt Step2: Alignment...575 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence...483 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str.=uc; # convert to uppercase $str.=su...} } } # Example usage my $dna = "GGATCCATGGCCTAGG"; # example DNA sequence...482 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared test o...############################### # Read sequence file 1 #####################...FAlite(\*FILE); # loop through each sequence...# to count dinucleotides, loop through sequence,...469 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 PRJNA880745468 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 / $...GCCTTACGCGCGCGCGC"; my $gc_content = calculate-gc-content($dna_sequence);...169 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...ssr, End: $ssr, Length: $ssr, Sequence:...169 days ago
Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) = @_; $sequence = uc($sequence); # Convert the sequence to uppercase my $gc_count = () = $sequence...n $gc_content; } # Example usage: my $dna_sequence =...154 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
def multi_to_single_line_fasta(input_filename, output_filename): try:...s output_file: current_sequence = "" for lin...# If a header line, write the previous sequence...'\n') current_sequence =...153 days ago
