[ensembl-dev] Reconstructing mRNA from transcript coordinates (human)

[Allan Kamau]

On 7/10/12, Allan Kamau <kamauallan at gmail.com> wrote:
> I would like to search for a predetermined non-palindromic motif at
> the 3' end of immature (pre) mRNA for specific human genes. Some of
> these genes are found on the negative strand.
> So far I have managed to obtain the nucleotide sequences using the
> coordinates provided by the transcript object as shown at the end of
> these text.
>
> How do I now "convert" these sequences into nucleotide representations
> of mRNA. Where the left most nucleotide will be at the 5' end and the
> right most nucleotide will be at the 3' end.
>
> 1)For positive strand genes - should I take reverse complement of
> these sequences.
>
> 2)For negative strand genes - should I use these sequences as they are.
>
>
>
> Below is the code to obtain the transcript coordinates and the
> nucleotide sequence using these readings.
>
>     my $stable_id  = $feature->stable_id();
>     my $seq_region = $feature->slice->seq_region_name();
>     my $start      = $feature->start();
>     my $end        = $feature->end();
>     my $strand     = $feature->strand();
>     my
> $slice=$slice_adaptor->fetch_by_region('chromosome',$seq_region,$start,$end,$strand);
> 	my $seq="";
>     if($slice)
>     {
> 		$seq=$slice->seq();
> 	
> 		print sprintf("%s: %s:%d-%d (%+d)",
> 			$stable_id, $seq_region, $start, $end, $strand
> 		);
> }
>


I think an RNA sequence transcribed from the DNA sequence obtained
from the transcript's object coordinates would be the reverse
compliment of this obtained DNA sequence.
After reverse complementing the sequence I would find and replace "T" with "U".

Is this correct?

Allan.