Protein Back Translation For Aneides Flavipunctatus

Question

[Maria]

Hi, I want to back translate a protein sequence using emboss backtranambig which is a part of nd5 in Aneides flavipunctatus, according to NCBI I must use this Genetic code table but when I use vertebrate mitochondria in the mentioned tool I got in the result some amino acids i.e Y,N, H ...

   >MNYMLIFNSSLMMSIFLLLIPLILNSTNNTSWYMFVKSSIKLSFIVSLLPLMIFLSQGMESTATNLNLFTIYNFNISFSMKIDQYSILFLPVALFVTWAILEFAMWYMSKDLMINQFFKYLLLFLIAMMILVTANNMFQLF

>EMBOSS_001
ATGAAYTAYATGYTNATHTTYAAYWSNWSNYTNATGATGWSNATHTTYYTNYTNYTNATH
CCNYTNATHYTNAAYWSNACNAAYAAYACNWSNTGGTAYATGTTYGTNAARWSNWSNATH
AARYTNWSNTTYATHGTNWSNYTNYTNCCNYTNATGATHTTYYTNWSNCARGGNATGGAR
WSNACNGCNACNAAYYTNAAYYTNTTYACNATHTAYAAYTTYAAYATHWSNTTYWSNATG
AARATHGAYCARTAYWSNATHYTNTTYYTNCCNGTNGCNYTNTTYGTNACNTGGGCNATH
YTNGARTTYGCNATGTGGTAYATGWSNAARGAYYTNATGATHAAYCARTTYTTYAARTAY
YTNYTNYTNTTYYTNATHGCNATGATGATHYTNGTNACNGCNAAYAAYATGTTYCARYTN
TTY

*What is wrong? why the back translation is not well? any suggestion? or another tool to do it ? *

Answer 1

[Michael]

These are not amino acids but ambiguity codes, see: http://droog.gs.washington.edu/parc/images/iupac.html Y for example means C or T. You get what you have requested and there is nothing wrong with the program. From your link:

Backtranambig reads a protein sequence and writes the nucleic acid sequence it could have come from. It does this by using nucleotide ambiguity codes that represent all possible codons for each amino acid.

If you don't want ambiguity you have to use Backtranseq: http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/ instead.

[Maria]

but in Backtranseq there is no vertebrate mitochondria option

[Michael]

There is possibly no codon usage frequency calculated for this organism and its mitochondria. For the ambiguity enabled backtranseq only the correct genetic code is necessary which is the same for mitochondria from a large range of taxa. the non-ambiguity backtranseq tries to give the most frequent codon for each amino-acid and therefore requires a codon usage frequency table.

What do you need the reverse translation for (cloning?), that's important to decide how to proceed. Possibly, you can just choose any of the bases indicated by the ambiguity code, or you could make your own codon frequency table from the known genes in the mitochondria.