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<p class=MsoNormal>Helloo:<o:p></o:p></p>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>I just subscribed to the group and found this old message related
to <a
href="http://www.compbio.dundee.ac.uk/pipermail/jalview-discuss/2009-June/000189.html">cDNA
codon alignments </a><o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Courier New"'><o:p> </o:p></span></p>
<pre><a href="http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss">rquiroga at fcq.unc.edu.ar</a> wrote:<o:p></o:p></pre><pre>><i> I am having three problems.<o:p></o:p></i></pre><pre>><i> <o:p></o:p></i></pre><pre>><i> One is the Translation of cDNA, which seems to not handle gaps <o:p></o:p></i></pre><pre>><i> correctly sometimes,<o:p></o:p></i></pre><pre>><i> (ATAAAG---GTTCCT) translates to (IKVP)<o:p></o:p></i></pre><pre>><i> (ATAAAA---GTTCCA) translates to (IKVP), missing the gap.<o:p></o:p></i></pre><pre><o:p> </o:p></pre><pre>Jim’s answer: <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>The translate cDNA function will exclude any gapped columns from the<o:p></o:p></pre><pre>translated protein alignment. Otherwise, gaps are introduced when codons<o:p></o:p></pre><pre>intersect but are misaligned.<o:p></o:p></pre><pre>e.g.<o:p></o:p></pre><pre>A-TAAAG<o:p></o:p></pre><pre>AATAA-G<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>becomes<o:p></o:p></pre><pre>-I-K<o:p></o:p></pre><pre>N-K-<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>><i> Also I get a "Please select at least three bases in at least one <o:p></o:p></i></pre><pre>><i> sequence in order to perform a cDNA translation." when I try to <o:p></o:p></i></pre><pre>><i> translate my entire cDNA codon alignment to protein. (Sequences: 154 <o:p></o:p></i></pre><pre>><i> Minimum Sequence Length: 314 Maximum Sequence Length: 365 Average <o:p></o:p></i></pre><pre>><i> Length: 351). Maybe too big?<o:p></o:p></i></pre><pre><o:p> </o:p></pre><pre>Jim’s answer was:<o:p></o:p></pre><pre>My guess is that you have one or two Ns in the region you are<o:p></o:p></pre><pre>translating. The translate cDNA routine complains when the effective<o:p></o:p></pre><pre>number of *defined* bases that have been selected for translation is not<o:p></o:p></pre><pre>divisible by three. This is partly because it doesn't know how to use an<o:p></o:p></pre><pre>N or an X (or ?) in a codon.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>My experience:<o:p></o:p></pre><pre
style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>1.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>Gaps in translation are kept correctly<o:p></o:p></pre><pre
style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>I have the same error message <i>"Please select at least three bases … “ </i>when I select the whole alignment for translation and this has nothing to do with N, X or “?” in a codon. <o:p></o:p></pre><pre
style='margin-left:.5in;text-indent:-.25in;mso-list:l0 level1 lfo1'><![if !supportLists]><span
style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>This very useful option is unfortunately not working for entire sequences or large chunk of positions. <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>If some trick is known for fixing this problem?<o:p></o:p></pre>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks<o:p></o:p></p>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>Alexey
Eroshkin, <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:10.5pt;font-family:Consolas'>Burnham
Institute for Medical Research<o:p></o:p></span></p>
<p class=MsoNormal><o:p> </o:p></p>
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