Hi,
i have a question that might be silly...
I need to find in a sequence in fasta format the coordinates corresponding to the reference sequence one.
The normal way to solve this would be aligning the new sequence to the reference one, but I don't know how to do that because they are both simple fasta files.
Someone has some suggestion?
Thanks in advance!
Detailed info:
I downloaded a virus reference sequence from ncbi and used it to align some bam files and call snps. I now have the list of the snps coordinates, and I would like to add to my data set another sequence from the same virus downloaded from NCBI. My problem is that the coordinates that the new fasta file I have are relative to the number of base in the sequence itself. I would need coordinates relative to the reference sequence, in order to check which bases the new sequence has in the snps coorrdinates.
I am working on a Mac OSX Snow Leopard, but I have access to a new Linux OS if needed.
i have a question that might be silly...
I need to find in a sequence in fasta format the coordinates corresponding to the reference sequence one.
The normal way to solve this would be aligning the new sequence to the reference one, but I don't know how to do that because they are both simple fasta files.
Someone has some suggestion?
Thanks in advance!
Detailed info:
I downloaded a virus reference sequence from ncbi and used it to align some bam files and call snps. I now have the list of the snps coordinates, and I would like to add to my data set another sequence from the same virus downloaded from NCBI. My problem is that the coordinates that the new fasta file I have are relative to the number of base in the sequence itself. I would need coordinates relative to the reference sequence, in order to check which bases the new sequence has in the snps coorrdinates.
I am working on a Mac OSX Snow Leopard, but I have access to a new Linux OS if needed.
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