How to predict amino acid sequence after a framshift deletion in the gene

Question

[inayat45shaikh]

Hello group, I want to predict amino acid sequence of gene after deleting a single nucleotide?

[Asaf]

Do you mean how to translate nucleotides to protein? transeq of EMBOSS is one way, must be other tools out there.

Answer 1

[willgilks]

Hi Inayat,

I've posted a few links to translation tools below. Get one nucleotide sequence for the full-length open-reading-frame without the deletion, and one with the deletion, preferably in fasta format. Put them both through the translate-tool. Ensure that you have the correct, in-frame start codon. The genetic code does change slightly in some genomes https://en.wikipedia.org/wiki/List_of_genetic_codes

http://web.expasy.org/translate/

https://www.ebi.ac.uk/Tools/st/

http://www.fr33.net/translator.php

http://www.bioinformatics.org/sms2/translate.html

http://bio.lundberg.gu.se/edu/translat.html

http://molbiol-tools.ca/Translation.htm

http://insilico.ehu.es/translate/

http://www.attotron.com/cybertory/analysis/trans.htm

http://www.bioline.com/media/calculator/01_13.html

https://hcv.lanl.gov/content/sequence/TRANSLATE/translate.html

http://biotools.umassmed.edu/cgi-bin/biobin/transeq

http://translatorx.co.uk/

http://in-silico.net/tools/biology/sequence_conversion

http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html

http://db.systemsbiology.net:8080/proteomicsToolkit/DNATranslator.html