Perl script to find coding regions in DNA sequences
...f a real exon and intron, respectively. Extremely different values of coding potential should be obtained with the two sequences: high values (positive) for coding protein sequences and low values (zero or even...2153 days ago
Biological Sequence handling with Perl !
...description of the object sub asString { my $self = shift; return $self->type . '(' . $self->length . ' residues)'; } # Concatenate two sequences together and return the resul...2179 days ago
Perl script to count number of Ns in a multifasta file !
...$n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n"; } } close(I); __END__ Note: Convert sequences in oneline first perl -pe '/...2142 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2142 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...($trimLen1_rev (\S+)(.*)/) { $seqid = $1; $sequences{$seqid}{desc} = $2; pus...d; } else { chomp $line; $sequences{$seqid}{seq} .= $line;...2138 days ago
2124 days ago
Installing Porechop on Ubuntu !
...ends --end_size END_SIZE The number of base pairs at each end of the read which will be searched for adapter sequences (d...2104 days ago
2073 days ago
Perl script to create a consensus of nucleotide sequences !
use strict; use warnings; my @instances = qw ( AAAAA ATCGA ATAAA ); my @instances2 = qw ( AAAAA AACGA ATAAA AGAAA AGAAA); print consensus(@instances),"\n";...2030 days ago
Pack a perl program with their dependencies on Ubuntu !
...Jit@jit.aber Sequence Tube Maps: displays multiple genomic sequences in the form of a tube mapBy Jit 5 days ago SequenceTubeMapsdisplaysmultiplegenomicsequencestubemapgraphmap github...1509 days ago