Sir,
 	 I am a postgraduate in Biochemistry. Iam working as a project 
assistant under Dr. Shekhar C. Mande,in laboratory of structural 
biology, CDFD,India.We are working on development of a threading 
algorithm, that includes an independant stage based on secondary 
structure alignment. In this regard we starting with the enegry 
contact matrices that were published on December 27,1999, in PNAS, 
as standard substitution matrices as represented that these  were 
tested in both threading and structure prediction. So I would like 
to get your suggestions on different queries.
 	 1. We are doing a dynamic programming based sequence alignment 
based on secondary structures using contact matrices as 
substitution matrices.But we have a doubt that since they are 
distance/environment based matrices and differ from BLOSUM/PAM 
matrices , the result will be obscure. So we want to find out a 
way to utilize the matrices. We need little detailed suggestion on 
this concept.
  	2.I want to get the information about RT units.

  I would like to get the clarifications from you,as it will be 
very much
  helpful for us to proceed with our analysis.
  Thank you sir,
  Yours Sincerely,
  P.Sravana Kumar.

  ========================
  P. Sravana Kumar
  c/o Dr. Shekhar C. Mande,
  Laboratory of Structural Biology,
  Center for DNA Fingerprinting and Diagnostics,
  ECIL Road,
  Nacharam 500 076,
  Hyderabad,
  India.

  Ph:  Lab: Direct: 040-27171442
       General: 040-27151344-1400
  e-mail:  sravan@www.cdfd.org.in
  =========================
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