Question: Identification of a given amino acid sequence in nucleotide sequence
0
gravatar for hana.parizkova
3.4 years ago by
hana.parizkova0 wrote:

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

translation sequence • 1.2k views
ADD COMMENTlink modified 3.4 years ago by mastal5112.0k • written 3.4 years ago by hana.parizkova0

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!

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by natasha.sernova3.5k

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.

ADD REPLYlink written 3.4 years ago by hana.parizkova0

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.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by natasha.sernova3.5k
0
gravatar for mastal511
3.4 years ago by
mastal5112.0k
mastal5112.0k wrote:

If you're working on Linux, there are BioPerl packages that have functions to do what you need.

ADD COMMENTlink written 3.4 years ago by mastal5112.0k

Thanks! Don't you happen to know the exact way how to do my job using BioPerl? I couldn't find any such function.

ADD REPLYlink written 3.4 years ago by hana.parizkova0
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