Aligning two fasta files with multiple sequences

Question

[Ammar Danazumi]

Hi! I am Aligning two fasta files with multiple sequences (~2000 seqs each) and I would like to keep only the perfect matches in a separate file for further analysis. Can someone help me with a code or an app to do that?

[GenoMax]

Use command line blast+ or blat along with a tab delimited format (e.g. -outfmt 6 or psl respectively). Parse the results to keep identical hits.

[Ammar Danazumi]

Dear GenoMax, Can you explain further please? because I am bit a lost. How do I indicate the inputs and the outputs file? Can you write help me with a more simpler description of the line of code like?

"blast+ inputfile.fasta > outputfile.fasta"

[swbarnes2]

Why don't you try on your own first? Figuring it out on your own is faster than waiting for someone to spoon feed you here.

[Ammar Danazumi]

I will love to do that? but I am completely lost and I dont understand your description above.

[GenoMax]

You will need to use blast+ from NCBI. You can find instructions here. This is the same package that you may have used on web at NCBI. You will need to use it on the unix command line though.

Using blat can be simpler in some ways but you will need to be reasonably proficient with using unix command line. You can find a user guide for blat here.

[Ammar Danazumi]

Thank you for very much.

[MSRS]

MAFFT has an option (Output orde) like this where the same sequences are aligned one after another.

[Ammar Danazumi]

Thank you.