Alternative translation tables for cDNA -> Protein

Is it possible to support alternative translation tables? Translating cDNA for invertebrate mitochondria results in protein sequence errors.

…d

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Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk

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Hello David,

I’m afraid this is not currently supported in Jalview. The ‘standard’ translation is hard-coded (in ResidueProperties.codonHash2) in such a way that it is not simple to use an alternative table (e.g. by injecting a script).

I had a look for an existing feature request for this but (to my surprise) didn’t find one. Will check with the team whether this is already on the to-do list.

Regards,

Mungo

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Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 10 July 2017 16:04:48
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Alternative translation tables for cDNA → Protein

Is it possible to support alternative translation tables? Translating cDNA for invertebrate mitochondria results in protein sequence errors.

…d

Email signature

University of Dundee shield logo

Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk

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The University of Dundee is a registered Scottish Charity, No: SC015096

The University of Dundee is a registered Scottish Charity, No: SC015096

Mmm, it is something we have discussed in the past, though not recently. It probably should be there.

G.

Hello David,

I’m afraid this is not currently supported in Jalview. The ‘standard’ translation is hard-coded (in ResidueProperties.codonHash2) in such a way that it is not simple to use an alternative table (e.g. by injecting a script).

I had a look for an existing feature request for this but (to my surprise) didn’t find one. Will check with the team whether this is already on the to-do list.

Regards,

Mungo

Email signature

University of Dundee shield logo

Mungo Carstairs
Jalview Computational Scientist

The Barton Group
Division of Computational Biology

School of Life Sciences

University of Dundee, Dundee, Scotland, UK

www.jalview.org

www.compbio.dundee.ac.uk
g.m.carstairs@dundee.ac.uk

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From: jalview-discuss-bounces@jalview.org jalview-discuss-bounces@jalview.org on behalf of David Martin (Staff) d.m.a.martin@dundee.ac.uk
Sent: 10 July 2017 16:04:48
To: jalview-discuss@jalview.org
Subject: [Jalview-discuss] Alternative translation tables for cDNA → Protein

Is it possible to support alternative translation tables? Translating cDNA for invertebrate mitochondria results in protein sequence errors.

…d

Email signature

University of Dundee
                          shield logo

Dr David M A Martin PhD FRSB
Senior Lecturer in Bioinformatics
School of Life Sciences, University of Dundee
+44(0)1382 388704 | d.m.a.martin@dundee.ac.uk

University of Dundee
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The University of Dundee is a registered Scottish Charity, No: SC015096

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On 17/07/2017 09:20, Mungo Carstairs (Staff) wrote:

-- 
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
School of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton
 

The University of Dundee is registered Scottish charity: No.SC015096 

Hi - thanks for pointing out the issue David.

Mmm, it is something we have discussed in the past, though not
recently. It probably should be there.

yes. Also surprised there wasn't an existing feature request. Must have
slipped my mind..

I'm afraid this is not currently supported in Jalview. The 'standard'
translation is hard-coded (in ResidueProperties.codonHash2) in such a
way that it is not simple to use an alternative table (e.g.
by injecting a script).

I seem to remember we were thinking about adding support for
exonerate-style codon tables, but then got distracted by the Ensembl
work. By rights we should really include support when we introduce
species tagging for sequences.. which may happen in September/Oct this
year..

Jim.

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On 17/07/2017 11:28, Geoff Barton wrote: