I am trying to use BLAST tool to screen my own genome sequences for specific genes.
I am lacking bioinformatics knowledge and would like a simple explantation on how to do this.
Briefly, I've been given the genomes of the strains I am working with and would like to check whether they carry some known genes (NCBI) for specific compounds.
Any clue on how to do this?
The best way is going for training videos on Youtube, for example:
https://www.youtube.com/watch?v=gKRDe7-l42M
https://www.youtube.com/watch?v=RzC-V67z5LA
In general, you need to do 2 steps:
1. Generate a custom database from your sequences (FASTA)
2. Run local BLAST search.
This software may assist you as it includes BLAST and provides quite a convenient graphical interface for it:
http://ugene.net/
Indeed, you can run this online at NCBI:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Translations&PROGRAM=tblastn&BLAST_PROGRAMS=tblastn&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&DATABASE=n/a&QUERY=&SUBJECTS=
I would first translate the coding sequences of your genes of interest and run them in a TBLASTN search against your genomes.
Best wishes, Ralf
Dear Evangelia Zioga
What I often do is use the "Align two sequences" option on NCBI Blastn.
Your query will be your genome and the Subject sequence will be the gene you are looking for.
I hope this helps!
Tamara
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