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Primer BLAST against local genome (Read 12472 times)
Sep 5th, 2014 at 10:19pm
Strangelove   Ex Member

 
Hi, i just install Ugene, now i am wondering if Ugene can preform a routine task. I need to primer BLAST against a genome i have in FASTA format. is this possible ? - i have added the genome to the DB
also i would like to BLAST a gene and see the flanking regions of that gene, can i control the number of visible nts to either side ? 
 
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Reply #1 - Sep 8th, 2014 at 5:20pm

German   Offline
Full Member

Posts: 118
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Quote:
Hi, i just install Ugene, now i am wondering if Ugene can preform a routine task. I need to primer BLAST against a genome i have in FASTA format. is this possible ? - i have added the genome to the DB

Hello. Unfortunately Primer-Blast is not supported by UGENE yet. We have planned this feature and it will be implemented in one of some future releases (not the
nearest one).

Quote:
also i would like to BLAST a gene and see the flanking regions of that gene, can i control the number of visible nts to either side ?

As I understood your task, you want to BLAST the gene's sequence in your BLAST database (created from one genome). And you are not interested in the found regions (BLAST results), but you are interested in regions (several nucleotides) located out of the BLAST results (left and right regions). And you don't know how to get these regions using UGENE. Am I right?

If yes: Is it true that this task can be solved using a simple find operation? You can open the genome sequence with UGENE and find the subsequence (the gene's sequence) in the genome. The regions on the left and right sides of the found result are the solution of the task.
 
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Reply #2 - Sep 9th, 2014 at 3:09pm
Strangelove   Ex Member

 
Thanks for the reply, the search function worked very well..
could i use primer3 to find a bunch of primers and then use blast+ search to get an E-value ? could this process be automated with workflow designer ?
 
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Reply #3 - Sep 9th, 2014 at 5:50pm

German   Offline
Full Member

Posts: 118
***
 
Sorry, but I don't understand your task. Could you describe it in more details?
Your input data are:
1) Genome sequence [G].
2) Gene sequence [g].
What is your goal?

As I understood, you try to do the following steps:
1) Create the BLAST database [DB] from G.
2) Search g in G using the find pattern functionality (CTRL+F in the sequence view). It gives the gene region [gr].
3) Pick primers for gr. It gives the primers regions [pr].
So, now you have pr - the regions (annotations) of primers in the source genome.

What do you want to do next? You want to BLAST something (g, or the sequence of gr, or the sequences of pr) in DB and get E-values.
 
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