batch tool for finding mitochondrial DNA polymorphisms

Hi,

I have a bioinformatics project that involves finding polymorphisms in
mitochondrial DNA (mtDNA).  The polymorphisms are typically denoted as
"reference base/position/polymorphic base", as in A750G.  I'd like to add a
software tool to our company website where a visitor could paste in a set of
mitochondrial genomes, and a reference sequence, and get back a list of
polymorphisms.  Something like:



>Seq1

A458G, T4899A....

>SEQ2

T678C, G6789C....

etc.



We sequence mitochondrial DNA for customers interested in learning about
their ancient ancestry.



The site will be freely available.  It will be attached to our company site,
www.argusbio.com, which is still in development at LunarPages.  The author's
name and an email link could be listed on the page.



A full-length genome is 16,569 bases long.  Typically two people will have
around 30 to 50 differences in their mtDNAs - more (but less than 100) if
they have very different ancestry (African vs European, for example).  These
polymorphisms determine the person’s mitochondrial haplogroup.



It would be very helpful if the program were able to determine which
haplogroup the mtDNA belongs in based on the list of polymorphisms.  I have
tables of diagnostic polymorphisms used for classing mt genomes.



It would also be very useful if there were an option to generate a fasta
file that consisted of just polymorphic sites.  So if someone put in 100
full-length genomes, and a reference genome, the output would be fasta
sequences where each base varied from the reference in at least one test
sequence.  This output would be much easier to align with CLUSTALW than the
full-length sequences, which are typically > 99% invariant.



I am looking for some ideas of how best to implement this web-based tool.



Thanks,

David B. Whyte, Ph.D.
Argus Biosciences, LLC
650-954-1055

[email protected]
www.argusbio.com

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