Results for "B"
Bio-Scripts
Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation conda install -c bioconda blast #Windows installation...p://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2....ler using the defaults, it should put BLAST under C:\Program Files\NC...1153 days ago
- #!/usr/bin/perl use strict; use warnings; #assign strings to variables my $DNA = "GATTACACAT";...and #print out the value of the variable and its length my $DNAleng...d codon in $modifiedDNA my $codon = substr($modifiedDNA,3,3); print...
2923 days ago
Count the frequency of base G in a given DNA sequence
#!/usr/bin/perl use strict; use warnings; my $DNA = "GAT...#for each letter in the sequence check if it is the base G #if 'yes' increment $countG while($currentPos < $DNAlength){ my $base = substr($DNA,$currentPos,...2923 days ago
- #!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #transcribe DNA to RNA - T changes to U...\n"; #find the reverse complement of $DNA using substitution operator #first - r...
2923 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matc...2923 days ago
Check if your coputer ready to use BioPerl
#!/usr/bin/perl use strict; use warnings; #bioperl example code use strict; use warnings; #make the bioperl module (class) accessible to your program use Bio::Seq; print"ok - ready to use Bio::Seq";2923 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot open $gb_rep...ranslation=")(.*)/) { # protein product begins print "Translatio...} else { print "Problems: end of translation produ...2923 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::Seq...'-format' => 'Fasta'); $out = Bio::SeqIO->newFh('-format' =>...2922 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every sequence in a folder # Directory of sequences $myDir = "/home/anjana/seqs"; # Output directory (...
2922 days ago
Perl script to Mutate a DNA Sequence
#!/usr/local/bin/perl -w # This script randomly mutates the DNA...ant\n"; print WRITE "$mutant\n"; } sub mutate { my($dna)...ition) = randomposition($dna); my $current_base = substr($dna, $position,...2922 days ago
