Align to fasta

[marco12345]

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.

[GenoMax]

Use "blat".

You can get the source from here: http://users.soe.ucsc.edu/~kent/src/ I assume you are an academic user.

Documentation here: http://genome.ucsc.edu/goldenPath/help/blatSpec.html

The "dabatase" and "query" can be two fasta files.

[sudhirvarma]

If you are comfortable with any of the common short-read aligners you can also use them, after making the corresponding index using your reference sequence. For example, using bowtie2

#Build index
bowtie-build myRefSeq.fasta myRef

#Align fasta file input.fasta to the reference
bowtie -t myRef input.fasta output.sam

The output will be in the file "output.sam" in SAM format

Sudhir