Identify genome-wide synteny with LASTZ alignment
...TE.lib_for_FF.fa FFChr1.txt Step2: Alignment using LASTZ and Chain/Net lastz AAChr1.txt FFChr1.txt K=2200 L=6000 Y=3400 E=30 H=0 O=400 T=1 --format=axt --out=chr01.axt axtChain...560 days ago
Perl script to find inverted repeats !
...Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $seqio = Bio::SeqIO->new(-file => $genome_file, -format => "fasta"); my $seqobj = $s...468 days ago
342 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
...output_file.write(current_sequence + '\n') print(f"Successfully converted {input_filename} to {output_filename} in single-line FASTA format.") except FileNotFound...138 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
...; close $input_file; close $output_file; print "Successfully converted $input_filename to $output_filename in single-line FASTA format.\n"; } # Example usage:...138 days ago
Bash script to convert Multi-line Fasta to Single-line Fasta !
...D {printf("\n");}' "$input_filename" > "$output_filename" echo "Successfully converted $input_filename to $output_filename in single-line FASTA format."138 days ago
137 days ago
Perl script for six frame translation !
...e Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $input_fasta = 'path/to/y...e input FASTA file my $seqio = Bio::SeqIO->new(-file => $input_fasta, -format => 'fasta'); my $sequence =...137 days ago
Python script for six frame translation of sequences !
...ame)} Translation:\n{protein_sequence}\n") # Replace 'path/to/your/input.fasta' with the actual path to your input nucleotide sequence in FASTA format input_fasta = 'path/to/your/...137 days ago
Perl script to parse VCF file !
#!/usr/bin/perl use strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl input.vcf\n" unless @ARGV; my $vcf_file = shift @ARG...137 days ago