How can icreate a local database and run a local blast operation using genome sequence?

I have to fasta file in my pc.

one is a fasta file having gene sequence : gene1.fas

another is a fasta file having whole genome sequence : genome1.fas

I am trying to run a local blast where gene1.fas FASTA file containing query nucleotide and genome1.fas is the local BLAST database.

For creating a local database I have run the code :

DB = blastformat('Inputdb', 'E:\genome1.fas');

but getting error :

Error using blastformat

Too many output arguments.

Later I run the fastaread() code to replace the fastafile with path into a specific name.

gene1 = fastaread('E:\gene1.fas');

genome1 = fastaread('E:\genome1.fas');

Then i have execute the blastlocal() code :

ABC = blastlocal('inputQuery',gene1,'program','blastn','database',genome1,'format',1,'tofile','E:\ABC.txt');

but getting error :

Error using blastlocal (line 161)

Invalid database name.

Will you help me to resolve the problems and how will i finally run the local blast operation.

Answer 1

[Paola Favaretto]

Try this:

>> blastformat('Inputdb', 'E:\genome1.fas');

You do not need an output variable (check the help for reference on the usage). Once the database is created, your blast search should work. Make sure you have writing permissions to create the database files.