Results for "Genome Sequence"
Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ h...ww.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['g...1134 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide...ani fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequences Rscript plotSeq.R seq1.fa s...1099 days ago
R script to visualize fastANI core-genome comparison
####### # Purpose: Visualize fastANI core-genome comparison # Usage: Rscript # Output: .pdf # Uses genoPlotR package: http://genoplotr.r-forge.r-project.org #Parse...1099 days ago
BioPerl to convert between sequence formats from Fasta to Genbank
#!/usr/local/bin/perl -w # Sequence formats to choose: Fasta, EMBL. GenBank, Swissprot, PIR and GCG use Bio::SeqIO; $inFile = "BRCA2.fa"; $in = Bio::SeqIO->newFh('-file' =...2914 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs.../home/anjana/patterns/polyA.pat"; # Go to sequence directory and open it (i.e, r...
2914 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA =...
2915 days ago
Count the frequency of base G in a given DNA sequence
#!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #initialize...e the length of $DNA my $DNAlength = length($DNA); #for each letter in the sequence check if it is the base G #i...2915 days ago
- #!/usr/bin/perl use strict; use warnings;...$DNA; $RNA =~ s/T/U/g; print "RNA sequence is $RNA\n"; #find the reve...ution operator #first - reverse the sequence my $rcDNA = reverse($DNA);...ation operator #first - reverse the sequence $rcDNA = reverse($DNA); #th...
2915 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genban...print "GI: $2\n"; } elsif (/(DEFINITION\s*)(.*)(\.)/) { print "Sequence name: $2\n"; } elsif...2915 days ago
Perl script to Mutate a DNA Sequence
#!/usr/local/bin/perl -w # This script randomly mutates the DNA sequence and generates 10 successive m...it asks for the file name of the DNA sequence. # If the DNA sequence file...nafile.txt # In Linux : /home/user/sequence/rnafile.txt use File::Path...2914 days ago
