Results for "sequences"
Bio-Scripts
Python script to download covid genome !
.../usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ ha...ests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text) seqs = seqs['ge...1121 days ago
Download genome using NCBI esearch command line !
...NI for alignment free comparision #conda install -c bioconda fastani fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequences Rscript plotSeq.R seq1.fa se...1086 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...1086 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"; # Output directory (re...
2900 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT"; my $polyA = "AAAA"; #concatenate two strings my $modifiedDNA =...
2901 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.com) use warnings; use strict; use Getopt::Long; use LWP::Simple; use URI::Esc...2900 days ago
Blast result parser with Perl and Bioperl
...cession . "\t"; # get the lengths of the hit sequences prin...gth . "\t"; # get the description of the hit sequences print OUT $hit->descripti...2899 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...elp\n". " -m: missing character\n". "Print out the name of sequences with characters other than AT...? to the ambigous characters.\n" . "If multiple files are given, sequences in all files are marged. If...2899 days ago
- ...$end; my $xml = get($URL_gene); my $xp = XML::XPath->new(xml=>$xml); my $nodeset = $xp->find('/DASDNA/SEQUENCE/DNA/text()'); # find all sequences # there should be only one n...
2894 days ago
Needleman-Wunsch Algorithm in Perl
...1998, Pg. 19 # Needleman-Wunsch global alignment algo (GOTHO 1982 mod) # usage statement die "usage: $0 \n" unless @ARGV == 4; # get sequences, matrix and gapcost from comm...2890 days ago
