<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Hardip,<div><br></div><div><blockquote type="cite"><div><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size: 11pt; ">However, normally a peptide should represent three nucleotides, but I am getting a two nucleotide codon (TC) for this position </span></font></div></blockquote><br><div>The evidence for that transcript is incomplete and the CDS ends with only two nucleotides TC in the last annotated codon.</div><div>You can check the CDS in the browser:</div><div><a href="http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000177000;r=1:11863076-11863097;t=ENST00000413656">http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000177000;r=1:11863076-11863097;t=ENST00000413656</a></div><div><br></div><div>Cheers,</div><div>Jana (Ensembl helpdesk)</div><div><br></div><div><br></div><div><br><div><div>On 9 Mar 2011, at 00:50, Hardip Patel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>
<font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">Hi All<br>
<br>
I am trying to identify the codon triplet in which a single nucleotide genomic position is involved in.<br>
<br>
Rephrased more elaborately, <br>
<br>
I have genomic loci chr1:11863085:11863085:-1 (chr start end and strand).<br>
This loci is overlapping with transcript ID: ENST00000413656.<br>
The loci is in the protein-coding (CDS) region of the transcript/cDNA.<br>
<br>
Therefore I first call transcript object by stable id using the transcript adaptor.<br>
Then I identify the peptide co-ordinates for the genomic loci by calling transcriptmapper.<br>
Once I get the peptide coordinate, I get the genomic coordinates for that peptide.<br>
<br>
Below is the script to do so.<br>
<br>
my $transcript_adaptor = $reg->get_adaptor("Human", "Core", "Transcript");<br>
my $slice_adaptor = $reg->get_adaptor("Human", "Core", "Slice");<br>
my $transcriptObject = $transcript_adaptor->fetch_by_stable_id("ENST00000413656");<br>
my $transcriptMapper = $transcriptObject->get_TranscriptMapper();<br>
my @pepCoords = $transcriptMapper->genomic2pep(11863085, 11863085, -1);<br>
foreach my $pepinfo (@pepCoords){<br>
my @pep2genomic = $transcriptMapper->pep2genomic($pepinfo->start, $pepinfo->end);<br>
print "Peptide = ". $pepinfo->start."\t". $pepinfo->end."\t". $pepinfo->id."\t". $pepinfo->length."\t". $pepinfo->strand."\n";<br>
foreach my $gc (@pep2genomic){<br>
my $codonSlice = $slice_adaptor->fetch_by_region("toplevel", 1 , $gc->start, $gc->end, $gc->strand);<br>
print "Genomic = ".$gc->start."\t".$gc->end."\t".$gc->id."\t".$gc->length."\t".$gc->strand."\t".$codonSlice->seq."\n";<br>
}<br>
}<br>
<br>
However, normally a peptide should represent three nucleotides, but I am getting a two nucleotide codon (TC) for this position and my script dies with following error message<br>
<br>
Can't locate object method "id" via package "Bio::EnsEMBL::Mapper::Gap".<br>
<br>
Could somebody please explain me what these gaps are? And also, how to overcome this issue of two/one nucleotide codons.<br>
<br>
Any help is greatly appreciated<br>
<br>
Thanking you<br>
<br>
Hardip<br>
</span></font>
</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jana Vandrovcova, Ph.D.<br>User Support Officer<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>United Kingdom<br></div></div>
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