I want a tool which gives a list of michondrial genes not nuclear genes against a perticular motif.
If you can work with the translated protein sequences there are several utilities available on the web that recognize the predicted mitochondrial transit peptide responsible for their import into the mitochondrion. You should try Protein Prowler (http://pprowler.itee.uq.edu.au/pprowler_webapp_1-2/index.jsp) or TargetP (http://www.cbs.dtu.dk/services/TargetP/)
MitoProt is another one (http://ihg.gsf.de/ihg/mitoprot.html) or the PSORT programmes at http://psort.hgc.jp/
However, most programmes are 'trained' using animal or fungal sequences (human, mouse, yeast) and might not recognise other organisms' mitochondrial targeting signals. In addition, several mitochondrial proteins don't use cleavable N-terminal signals and those are hard to predict.
So, another strategy is to BLAST your predicted proteins against known mitochondrial proteomes. Combined with the above, you'll get a better idea what might be in your mitochondrion.
However, if you meant genes present on mitochondrial genomes, then the above (including Fred's one) don't work. Although you talk about motifs, both of us assume you meant nuclear encoded but mitochondrial targeted. If not, then it might be best to check the mitochondrial genome content of a related species and BLAST your genome with the few genes present on the mitochondrial genome. You might miss a few. In this case, the best strategy is to isolate mtDNA and just sequence it.
Hope this helps!
if u are going to study about taxonomical characters of a single species , then u can go for studying mitochondria gene sequences . otherwise it is very hard to collect 10 species and to select particular gene markers and then use correct protocols to get best results . if can try it , ALL THE BEST.
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