Hello,
I have a set of nucleotide sequences and I need to locate and extract parts of it which are translated into given short amino acid sequence (say for example GGATG). I was sure that there definitely must exist an online tool for that, but the only one I could find was part of Sequencher programme: https://www.genecodes.com/sequencher-features/next-generation-sequencing/find-amino-acides. Unfortunately, Sequencher is only available for Windows and Mac, but I am working on Linux.
Does anybody have a tip how to do my job easily?
Thanks, Hana
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hana.parizkova •
Thanks! Don't you happen to know the exact way how to do my job using BioPerl? I couldn't find any such function.
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I would use tblastx. It should give you a translation in 6 frames.
Below you will find the information about all existing Blast-programs.
http://blast.ncbi.nlm.nih.gov/Blast.cgi
1) First you need to make a database of your nucleotide sequences. To do it:
makeblastdb -in input_file (file name of the contigs or whatever) -dbtype nucl (if nucleotide) -out dbname (the database name)
2) Run the blast-program:
tblastx -query input (with the genes file) -db (database name, which was created in step 1) -out outname (file name with
the results)
I would use tblastx for your task.
If you would like to search the database using a protein query,
use tblastn, but in practice tblastx usually finds more sequences...
Good luck!
Thanks, but tblastx wouldn't work in my case. I don't need the translation of the whole sequence (in fact I already have it), I just need to extract the nucleotides which are translated into a given short sequence.
I repeat my two strings:
If you would like to search the database using a protein query,
use tblastn. I hoped it might be useful. It looked easy.