[Bioperl-guts-l] bioperl-live/Bio/Tools CodonTable.pm,1.30,1.31

Brian Osborne bosborne at pub.open-bio.org
Thu Sep 29 09:06:05 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory pub.open-bio.org:/tmp/cvs-serv973/Bio/Tools

Modified Files:
	CodonTable.pm 
Log Message:
NCBI's Codon Table page has changed


Index: CodonTable.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/CodonTable.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** CodonTable.pm	27 Sep 2005 13:08:46 -0000	1.30
--- CodonTable.pm	29 Sep 2005 13:06:03 -0000	1.31
***************
*** 59,66 ****
  =head1 DESCRIPTION
  
! Codon tables are also called translation tables or genetics codes
! since that is what they try to represent. A bit more complete picture
  of the full complexity of codon usage in various taxonomic groups
! presented at the NCBI Genetic Codes Home page.
  
  CodonTable is a BioPerl class that knows all current translation
--- 59,66 ----
  =head1 DESCRIPTION
  
! Codon tables are also called translation tables or genetic codes
! since that is what they represent. A bit more complete picture
  of the full complexity of codon usage in various taxonomic groups
! is presented at the NCBI Genetic Codes Home page.
  
  CodonTable is a BioPerl class that knows all current translation
***************
*** 78,85 ****
  translating. Its default for output is DNA.
  
! Note: This class deals primarily with individual codons and amino
!       acids. However in the interest of speed you can L<translate>
!       longer sequence, too. The full complexity of protein translation
!       is tackled by L<Bio::PrimarySeqI::translate>.
  
  
--- 78,87 ----
  translating. Its default for output is DNA.
  
! Note: 
! 
! This class deals primarily with individual codons and amino
! acids. However in the interest of speed you can L<translate>
! longer sequence, too. The full complexity of protein translation
! is tackled by L<Bio::PrimarySeqI::translate>.
  
  
***************
*** 117,121 ****
  
  NCBI Genetic Codes home page:
!      http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=c
  
  EBI Translation Table Viewer:
--- 119,123 ----
  
  NCBI Genetic Codes home page:
!      http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
  
  EBI Translation Table Viewer:
***************
*** 125,129 ****
       ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/
  
! Thank your for Matteo diTomasso for the original Perl implementation
  of these tables.
  
--- 127,131 ----
       ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/
  
! Thanks to Matteo diTomasso for the original Perl implementation
  of these tables.
  



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