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
--------------------------------------------------

Dear Albert,


wrote on Apr 14^th, 2005 at 6:50am:

Hi all, I would love to have some more codon tables in hyphy: for example, for bacterial genomes.

I took the liberty of moving your message from the 'Bugs' forum to the 'New Features' forum, as it seemed more appropriate.

I'll update the list of standard genetic codes to include all those currently listed on the NBCI taxonomy page. Note that unless a genetic code has different stop codons from on of those already defined, from the perspective of codon substitution models there is no difference between the two (initiation codons are not treated in a special way).

Also, while I put together the update (will take me a few days to get around to it, sadly), you may want to take a look at the bottom of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for a set of instructions on how one can add a custom genetic code to standard analyses.

For all analyses done through the graphical interface, you can define genetic codes by calling File->New->New Genetic Code from the console window.

I'll post a note when the list of standard genetic codes has been updated and where it can be downloaded from.

HTH,
Sergei

Will selenoproteins be treated as a normal aa in hyphy?

I found out that some programs choke up with them, and there are a few of them in some prokaryotes I'm studying.

Dear Albert,


wrote on Apr 18^th, 2005 at 5:30am:

Will selenoproteins be treated as a normal aa in hyphy?

The standard set of protein models in HyPhy is configured to recognize only 20 basic aminoacids; therefore sites with seleoncysteines will most likely be skipped. It is easy to instruct HyPhy to allow the 21st state, however one must modify existing models to define the rates to/from the 21st state. Are there any non-trivial (e.g. not the protein version of F81) evolutionary models which incorporate selenocysteine?

If you are interested in developing such models in HyPhy it should be easy to get started - let me know if you want to give it a try.

HTH,
Sergei

After double-checking, I found out that the "Bacterial and Plant Pastid" code is the same as the "Universal" exceptuating the fact that it has 3 more start codons.

As it seems that start codons are not considered differently as middle-gene codons, they are identical.

Dear Albert,


wrote on May 3^rd, 2005 at 8:43am:

After double-checking, I found out that the "Bacterial and Plant Pastid" code is the same as the "Universal" exceptuating the fact that it has 3 more start codons. As it seems that start codons are not considered differently as middle-gene codons, they are identical.

That is indeed correct; start codons are treated the same way all other codons in the gene are - at least in the models we have implemented currently.

Cheers,
Sergei