matrix - Mathematica SequenceAlignment SimilarityRules -

in mathematica's option similarityrules http://reference.wolfram.com/mathematica/ref/similarityrules.html sequencealignment http://reference.wolfram.com/mathematica/ref/sequencealignment.html possibility of pushing simmilarity matrix - "blast" "blosum62" "blosum80" "pam30" "pam70" "pam250". if want use own ones? have define {{a_,a_}->1,{a_,b_}->-1} etc each combination of letters?? or there possibility of writing own , storing matrix, importing it? quickest option of defining such object using mathematica's matrices?

any appreciated,

cheers, m.

i did grep on 'blosum' (one of named similarity rules matrices) see it's defined , in hope of discovering mechanism implementation. found seems defined in file called similarityscorematrices.mx, binary mathematica file, equivalent object file in compiled language. looked files "blosum' in found none. looks wolfram did not intend these names extended, since if did mechanism discoverable in documentation or @ least kind of hunting did.

however, can still want. if build rules list, can use dumpsave[] write binary image, , use get[] read them back.

one final note, similarityrules awful lot mathematica's sparsearray rules. wouldn't surprised find named similarity rules matrices sparsearrays. might you're not losing efficiency passing rules in on mathematica doing matrices. might can pass in sparearray, isn't documented way , haven't tried it.