How To Get The Mutation List For Mtdna Complete Sequence Submitted In Genbank?

Question

[User 1793]

I am looking for some script which provide the difference from r-CRS to the mtDNA human genome, directly from the GenBank!

e.g. I have a genbank id GQ337588.1

now I search in NCBI and get the fasta file there, after that I need some software which tells me the summary of the difference of this sequence with r-crs.

in above case the differences are-

A73G A263G 315.1C T489C T711C A750G A1041G A1438G A2706G T3394C
G4491A A4769G 5899.1C C7028T T7142C G7697A A8701G A8860G A9242G T9540C
A10289G A10398G C10400T T10873C G11719A C12705T T14308C A14417G C14766T T14783C G15043A G15301A A15326G G15927A C16223T C16234T A16316G T16362C

Thanks for any help.

regards

Answer 1

[Damian Kao]

You can write a script with bioperl using efetech to get the sequence from NCBI: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

And use BioPerl's simple alignment to align the two sequences for a list of mismatches/gaps: http://www.bioperl.org/wiki/HOWTO:AlignIO_and_SimpleAlign

I am not aware of any pre-written scripts/software that'll do what you want. Perhaps other people will have suggestions.

Answer 2

[haansi]

Although this is an older question - maybe this can still be useful: you can use the GenBank mtDNA Sequence Checker on Ian Logans Website: http://www.ianlogan.co.uk/checker/genbank.htm or use Web-Tools such as mitomaster: http://mitomaster.research.chop.edu/MITOMASTER or MitoTool http://www.mitotool.org/