[BiO BB] Ka/Ks

D. Norris dmnunif at charter.net
Sun Jun 27 12:07:51 EDT 2004


Sorry, our corporaton can not help you. 

Our research in bioinformatics is on the electrochemistry by which proteins transduce environmental chemical groups or energy into information in living cells or multicellular organisms.

  ----- Original Message ----- 
  From: Peter Groenen 
  To: bio_bulletin_board at bioinformatics.org 
  Sent: Friday, June 25, 2004 5:27 PM
  Subject: [BiO BB] Ka/Ks

  I am looking for a command line tool that can handle protein alignments as input and aligns the corresponding transcripts. I want to use it for Ka/Ks determination.
  Secondly, I need something like a "sliding " Ka/Ks determination to see if there is a difference within a protein when looking at smaller segments. 
  I looked at SNAP, and also PAML but they are not very straightforward in use, especially hte diffenret formats are giving me trouble.
  Any ideas?
  Thanks in advance.
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