Hello to all,
I have a complete genome of a plant and a fast file with multiple sequences of a specific protein ( nucleotide sequence). I want to blast the file into the genome to see if these proteins are present there. In bioedit i can blast one sequence at the time, but that is time consuming. What is the best program to do it, to take the fasta file and blast it againt the genome? I have access to DNAstar lasergene...any of the programs to it?
Thanks to all.
Hi! You can create a multifasta file with all proteins you want to blast
Then you can run tblastn
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
check "Align two or more sequences "
Fasta file with proteins will be a query, your genome - subject
If your genome already at NCBI database it will be faster just indicate its accession number, than reload all sequence.
Abhijeet Singh and Timur Yergaliyev thank for your replies. However, can I Use NCBI blast with my reference genome? I want to do a "local Blast". Multiple files in NCBI I now how to do it. My question is How can I creat a local database with my reference genome and use It do to blast with my query sequences
If you use linux or unix like system, you can make local database is just oneliner code.
- download blast+ executable and install
- make database with command
$ makeblastdb -in genomefastafile -dbtype nucl -title yourtitle -out yourpath/yourtitle
- then run blast command, if you want to do tblastn or any blast
$ tblastn -query inputfasta -db yourtitle -out outputfile.csv -outfmt "7"
https://www.ncbi.nlm.nih.gov/books/NBK279690/
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