Results for "Paired end sequencing"
Bio-Scripts
# To follow these instructions, we'll assume your system admins have already installe....24.1/lib/perl5 make make install # Install dependencies for Ensembl API, VEP, O....1/bin:$PATH" # You can add those 2 lines to the end of you...2145 days ago
Count the frequency of base G in a given DNA sequence
#!/usr/bin/perl use strict; use warnings; my $DNA = "GATTACACAT"; #initialize $countG and $currentPos m...DNA,$currentPos,1); if($base eq "G"){ $countG++; } $currentPos++; } #end of whi...2918 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cann...ex: CDS 357..1541 $cds_start = $2; $cds_end = $4; print "CDS: $cds_start - $cds_end\n";...2918 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w #################################################### #MLP neural network in Perl Or...umHidden = 4; my $LR_IH = 0.7; my $LR_HO = 0.07; ################ Data dependent set...2917 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely di...re, query frame, query start, query end, hit start, hit end, positives, and identical #...\tquery_start\t"; print OUT "query_end\thit_start\thit_end\tpositive...# get the start and the end of the...2915 days ago
- #!/usr/bin/env perl use strict; use warnings; use LWP::Simple; use XML::XPath;...chomp $size; my $start = $pos - ($size/2); my $end = $pos + ($size/2); # Fi...nt=chr"; $URL_gene .= $chr . ":" . $start . "," . $end; my...
2911 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; l...)/; my ($header) = "$/$1_$start-$end\n"; my $seq = ${^POSTMAT...print +( substr $seq, $start - 1, $end ) . "\...2622 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2618 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2469 days ago
Genetic Algorithms demonstration with word DNA in Perl
#!/usr/bin/perl -w # GA demonstration with word DNA (512 bits) use strict; use Dat...ord we accept # you can use any word list at the end of the program # do the @d...ubstring, that's OK) # increment the fitness depending on...2373 days ago
