Results for "go"
Bio-Scripts
Install BLAST in Ubuntu/Linux and Window !
...a blast #Windows installation First: Download ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7...If that FTP links does not work, try HTTP instead http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7...1130 days ago
Parse a genbank file using regular expressions
...{ # protein product begins print "Translation: "; $protein = $2; $trans = 1; } elsif ($trans) { # translation still going on if (!/"/) { #...2901 days ago
- ...Path to pattern file $patFile = "/home/anjana/patterns/polyA.pat"; # Go to sequence directory and ope...ead contents) chdir($myDir) || die "Cannot change to $myDir: $!"; # Go to $myDir opendir(DIR, ".")...
2900 days ago
Perl script to Mutate a DNA Sequence
...NCE:= "; $dnafilename = ; chomp $dnafilename; unless ( open(DNAFILE, $dnafilename) ) { print "Cannot open file \"$dnafilename\"\n\n"; goto h; } my $DNA = ; close D...2900 days ago
Retrieve NCBI GenBank records with a range of accession numbers
...returnType => undef, maxRecords => undef, format => undef, verbose => undef, url => 'http://www.ncbi.nlm.nih.gov/entrez/eutils', retries...2900 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...C-.\n". "If -m is specified, the ambiguous characters are repleced with the\n". "specified character. e.g. -m '?' will place ? to the ambigous characters.\n" . "If m...2898 days ago
Needleman-Wunsch Algorithm in Perl
...GHEE PAWHEAE BLOSUM50.txt -8 # See: "Biological sequence anaysis" Durbin et al. ed. CUP 1998, Pg. 19 # Needleman-Wunsch global alignment algo (GOTHO 1982 mod) # usage state...2889 days ago
Count GC Content in nucleotide sequence with Perl
...#ARGV == -1) { usage(); exit; } $fasta_file = $ARGV[0]; $out_file = "gc_out.txt"; unless ( open(IN, "$fasta_file") ) { print "Got a bad fasta file: $fasta_fil...2889 days ago
Calculate ATGC percentage in parallel with perl
...d finishes up so we can # get it's exit code $pm->run_on_finish ( sub { my ($pid, $exit_code, $ident) = @_; #print "** $ident just got out of the pool "....2640 days ago
Calculate some statistics for a DNA alignment with Perl
...f synonymous /nonsynonymous substitutions ## my $in = Bio::AlignIO->new(-format => 'fasta', -file => 't/data/nei_gojobori_test.aln'); my $alno...2633 days ago
