Hi,
I've been working on a mitochondrial genetics project, and I'd like to
see a human mitochondrial-specific translation function integrated into
BioHaskell.
Here is a link to the NCBI human mitochondrial translation table:
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG2
I see that Bio.Sequence.Phd has a standard translation table, so I've
made a version called trans_tbl_mito with the appropriate changes
integrated. I know that there is a lot of re-factoring going on, and
I'm not sure what is the most efficient/elegant way to introduce this
feature.
Thoughts?
Dan
trans_tbl :: [(String,Amino)]
trans_tbl = [("GCT",Ala),("GCC",Ala),("GCA",Ala),("GCG",Ala),
("CGT",Arg),("CGC",Arg),("CGA",Arg),("CGG",Arg),("AGA",Arg),("AGG",Arg),
("AAT",Asn),("AAC",Asn),
("GAT",Asp),("GAC",Asp),
-- ("RAT",Asx),("RAC",Asx), -- IUPAC: R is purine (A or G)
("TGT",Cys),("TGC",Cys),
("CAA",Gln),("CAG",Gln),
("GAA",Glu),("GAG",Glu),
-- ("SAA",Glx),("SAG",Glx), -- IUPAC: S is C or G
("GGT",Gly),("GGC",Gly),("GGA",Gly),("GGG",Gly),
("CAT",His),("CAC",His),
("ATT",Ile),("ATC",Ile),("ATA",Ile),
("TTA",Leu),("TTG",Leu),("CTT",Leu),("CTC",Leu),("CTA",Leu),("CTG",Leu),
("AAA",Lys),("AAG",Lys),
("ATG",Met),
("TTT",Phe),("TTC",Phe),
("CCT",Pro),("CCC",Pro),("CCA",Pro),("CCG",Pro),
("TCT",Ser),("TCC",Ser),("TCA",Ser),("TCG",Ser),("AGT",Ser),("AGC",Ser),
("ACT",Thr),("ACC",Thr),("ACA",Thr),("ACG",Thr),
("TAT",Tyr),("TAC",Tyr),
("TGG",Trp),
("GTT",Val),("GTC",Val),("GTA",Val),("GTG",Val),
("TAG",STP),("TGA",STP),("TAA",STP)
]
trans_tbl_mito :: [(String,Amino)]
trans_tbl_mito = [("GCT",Ala),("GCC",Ala),("GCA",Ala),("GCG",Ala),
("CGT",Arg),("CGC",Arg),("CGA",Arg),("CGG",Arg),("AGA",STP),("AGG",STP),
("AAT",Asn),("AAC",Asn),
("GAT",Asp),("GAC",Asp),
-- ("RAT",Asx),("RAC",Asx), -- IUPAC: R is purine (A or G)
("TGT",Cys),("TGC",Cys),
("CAA",Gln),("CAG",Gln),
("GAA",Glu),("GAG",Glu),
-- ("SAA",Glx),("SAG",Glx), -- IUPAC: S is C or G
("GGT",Gly),("GGC",Gly),("GGA",Gly),("GGG",Gly),
("CAT",His),("CAC",His),
("ATT",Ile),("ATC",Ile),("ATA",Met),
("TTA",Leu),("TTG",Leu),("CTT",Leu),("CTC",Leu),("CTA",Leu),("CTG",Leu),
("AAA",Lys),("AAG",Lys),
("ATG",Met),
("TTT",Phe),("TTC",Phe),
("CCT",Pro),("CCC",Pro),("CCA",Pro),("CCG",Pro),
("TCT",Ser),("TCC",Ser),("TCA",Ser),("TCG",Ser),("AGT",Ser),("AGC",Ser),
("ACT",Thr),("ACC",Thr),("ACA",Thr),("ACG",Thr),
("TAT",Tyr),("TAC",Tyr),
("TGG",Trp),
("GTT",Val),("GTC",Val),("GTA",Val),("GTG",Val),
("TAG",STP),("TGA",Trp),("TAA",STP)
]
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