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Hi Andrés<br>
<br>
The Mapper returned by the GenomicAlign object maps between two
coordinate types called "sequence" and "alignment". I believe in
your case, $type should be "sequence".<br>
<br>
You may want to consider usng the map_coordinates() method rather
than the list_pairs() one. The map_coordinates() method will trim
the mappings such that they match your query region (start and end
of the gene) while list_pairs() will return all the pairs that
overlap. Also, list_pairs() returns a reference to an array, not the
start position of the 1st mapping.<br>
<br>
I hope this helps<br>
<br>
Javier<br>
<br>
<div class="moz-cite-prefix">On 02/04/13 18:30, Andrés Arturo Lanzós
Camaioni wrote:<br>
</div>
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cite="mid:CAGA5+WcrywB3Fcxxj90PbG3310+2ETUjNSHa+4zoBs2_Kf1BCQ@mail.gmail.com"
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<div><font><span
style="font-family:arial,helvetica,sans-serif">Hi.<br>
</span></font></div>
<font><span
style="font-family:arial,helvetica,sans-serif"><br>
My name is Andrés Lanzós and I am using
the Ensembl API for the first time.<br>
</span></font></div>
<font><span
style="font-family:arial,helvetica,sans-serif"><br>
I want to map genes from primates in a
genomic align. <br>
<br>
<font>First</font>, <font>I</font> <font>use</font>
the method get_Mapper () to transform the
coordinates f<font>rom each original
sequence to <font>th</font>e alignment.</font></span></font><br>
<br>
<pre>$this_mapper = $genomic_align->get_Mapper();
</pre>
<br>
</div>
Then, I use the method list_pairs () to find the
coordinates for each gene in the alignment.<br>
<br>
<pre>my $start0=$this_mapper->list_pairs($gene_id,$gene_start,$gene_end,$type);
</pre>
</div>
But I have a problem with the fourth argument:
$type, i do not know which value to put.<br>
<br>
</div>
</div>
Could yo help me with this?<br>
<br>
My final objective is to extract the common regions
between the genes for the different species of the
alignment.<br>
<br>
</div>
Thank you.<br>
<br>
</div>
Kind regards,<br>
</div>
Andrés Lanzós.</div>
</div>
<br>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK</pre>
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