Aligning two fasta files with multiple sequences

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2.8 years ago

Ammar Danazumi ▴ 10

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?

Protein Fasta Sequence Alignment • 1.7k views

ADD COMMENT • link 2.8 years ago by Ammar Danazumi ▴ 10

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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.

ADD REPLY • link 2.8 years ago by GenoMax 141k

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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"

ADD REPLY • link 2.8 years ago by Ammar Danazumi ▴ 10

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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.

ADD REPLY • link 2.8 years ago by swbarnes2 14k

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

ADD REPLY • link 2.8 years ago by Ammar Danazumi ▴ 10

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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.

ADD REPLY • link 2.8 years ago by GenoMax 141k

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Thank you for very much.

ADD REPLY • link 2.8 years ago by Ammar Danazumi ▴ 10

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