Results for "vi"
Bio-Scripts
Retrieve NCBI GenBank records with a range of accession numbers
...retries} >= $param{maxRetries} ) { die("Too many failures--giving up search."); }...cords} ) { message( $param{verbose}, "Retrieving $param{maxRecords} records...2916 days ago
Perl to print indivisual nucleotide from a sequence!
#!/usr/bin/perl use strict; use warnings; my $string = "ATGCTTGCGT?AAATG??CT?GCGTA"; my @chars = split("", $string); print "First character: $chars[0]\n";2914 days ago
Needleman-Wunsch Algorithm in Perl
#!/usr/bin/perl # USAGE: perl nw.pl HEAGAWGHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needlema...2905 days ago
Count GC Content in nucleotide sequence with Perl
...print OUT "ID\t% GCContent\tTotal Count\tG Count\tC Count\tA Count\tT Count\n"; $seq = ""; while () { chomp; if (/^>/) { #finish up previous line. if (length($seq) >...2905 days ago
- ...perl #use strict; #use warnings; #Author: Santhilal Subhash #Contact: santhilal.subhash@gu.se #RPKM for RNAseq V1.3 #USAGE for sample input provided: perl rpkm_script_beta.pl...
2871 days ago
BASH script for SelfBLAST a genome
...#USAGE: ./selfBlast.sh all #Common settings FASTAFILE=MergedContigs.fasta MYDB=myDB OUTFILE=seeRES THREAD=20 SEQ="" echo "User $USER provided $# arguments, Detail of th...2652 days ago
Download the genome from NCBI using bash script/command
...y summary and extract the URL # USER need to provide the right summary file to c...c.fna.gz|' > genomic_file_invertebrate # -for viral curl 'ftp://ftp.ncbi.nlm....(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_viral #Read the url from file...2532 days ago
Download the gff files from NCBI using bash script/command
...y summary and extract the URL # USER need to provide the right summary file to c...c.gff.gz|' > genomic_file_invertebrate # -for viral curl 'ftp://ftp.ncbi.nlm....(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_viral #Read the uerl from fil...2523 days ago
Genetic Algorithms demonstration with word DNA in Perl
...= shift @_; foreach my $individual (@$population) { # set...+; } else { $individual->{fitness} = 0 } }...sure we have at least one individual with # parent > 0...is not matched in the DNA, or vice versa next unless $word...2371 days ago
Create genome scaffolding with Perl
...} } @ARGV = @pslFiles; if(!$projOpts->{"query"}){ pod2usage({-exitVal => 1, -message => "Error: No query assembly file provided", -verbose =...2308 days ago
