Albert Vilella
Guest
|
Hi all,
first of all: congratulations for the program!
Second of all: I would love to have some more codon tables in hyphy: for example, for bacterial genomes.
Appended are the tables found in bioperl under: /Bio/Tools/CodonTable.pm
@NAMES = #id ( 'Standard', #1 'Vertebrate Mitochondrial',#2 'Yeast Mitochondrial',# 3 'Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma',#4 'Invertebrate Mitochondrial',#5 'Ciliate, Dasycladacean and Hexamita Nuclear',# 6 '', '', 'Echinoderm Mitochondrial',#9 'Euplotid Nuclear',#10 '"Bacterial"',# 11 'Alternative Yeast Nuclear',# 12 'Ascidian Mitochondrial',# 13 'Flatworm Mitochondrial',# 14 'Blepharisma Nuclear',# 15 'Chlorophycean Mitochondrial',# 16 '', '', '', 'Bacterial with selenocystein', # 19 'Standard with selenocystein', # 20 'Trematode Mitochondrial',# 21 'Scenedesmus obliquus Mitochondrial', #22 'Thraustochytrium Mitochondrial' #23 );
@TABLES = qw( FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCUWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG );
@STARTS = qw( ---M---------------M---------------M---------------------------- --------------------------------MMMM---------------M------------ ----------------------------------MM---------------------------- --MM---------------M------------MMMM---------------M------------ ---M----------------------------MMMM---------------M------------ -----------------------------------M---------------------------- '' '' -----------------------------------M---------------------------- -----------------------------------M---------------------------- ---M---------------M------------MMMM---------------M------------ -------------------M---------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- '' '' ---M---------------M------------MMMM---------------M------------ ---M---------------M---------------M---------------------------- -----------------------------------M---------------M------------ -----------------------------------M---------------------------- --------------------------------M--M---------------M------------ );
Thanks in advance,
Albert. Albert J. Vilella avilella_at_ub_edu -------------------------------------------- Departament de Genetica Universitat de Barcelona Diagonal 645 08028, Barcelona Tel: +34 934035306 Fax: +34 934034420 -------------------------------------------- avilella_at_ebi_ac_uk EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom --------------------------------------------------
|