<html><head><style type="text/css">body{font:12px Arial;margin:3px;overflow-y:auto;overflow-x:auto}p{margin:0px;}blockquote, ol, ul{margin-top:0px;margin-bottom:0px;}</style></head>
<body><div style="display: block; font-family: Arial; font-size: 12px;"><pre>short discussion of your ideas:<br><br>> 1) If you are sure you are not using ambiguous characters anywhere else<br>in <br>> your sequence you could have sequence class that treats any ambiguity<br>codes<br>> <br>> as polymorphisms and a SeqIO class that does the output formatting: r =><br><br>> a/g.<br>> <br><br>I would need to augment the ambiguity code to represent<br>deletions/insertions, right ? And this not trivial/hardly possible because<br>you need to define each combination A/_, C/_, and so on and if the deletion<br>concerns more than one base you need to explicitly model each combination.<br><br>> 2. Use sequence features like they do in EMBL/GenBank/DDJB feature tables<br>> to <br>> annotate mutations in the reference sequence.<br>><br><br>Seems most promising... But need to implement most.<br><br>> 3. Use Bio::Variation::SeqDiff to hold your reference sequence and<br>annotate<br>> <br>> polymorphisms as Bio::Variation::DNAMutation objects that can in turn<br>hold <br>> moltiple Bio::Variation::Allele objects.<br><br>To be sure: What is the intended way to represent Deletion, Insertions ?<br><br>this one:<br><br>defining 2 allele objects (note, the first allele has an empty sting as<br>-seq attribute)<br><br>$allele1 = Bio::Variation::Allele->new (<br> -seq => '',<br> -id => $id1,<br> -alphabet => 'dna',<br> -is_reference => 1<br>);<br><br>$allele2 = Bio::Variation::Allele->new (<br> -seq => 't',<br> -id => $id2,<br> -alphabet => 'dna',<br> -is_reference => 1<br>);<br><br>and assigning it to a mutation object:<br><br>$dnamut->allele_ori($allele1);<br>$dnamut->add_Allele($allele2);<br><br>for an insertion respective vice versa in the case of a mutation. Is that<br>right ? Cause when try create an empty Allele object and try to add an<br>empty string via $allele1->seq('') I get a warning.<br><br>Any comments are welcome :)<br><br>Regards,<br>Marian</pre></br><p style="margin-top:11px;padding-top:3px;background-image: url(http://mail.lycos.co.uk/Images/Mail/_content/dot.gif);background-repeat: repeat-x;background-position: 0px 0px;">Brauchst du eine Schocktherapie gegen den Alltag? Lächle! Die warme Sonne von Ibiza und ein bisschen Sand vom Mittelmeer ist die Therapie, die du brauchst. Plan deinen Urlaub in Spanien auf <A href="http://ad.de.doubleclick.net/clk;35699835;12983555;d?http://www.spain.info/TourSpain/Destinos/Provincias/D/KH/0/Ibiza?language=de"> www.spain.info </a></div></body></html>