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Hardware for sequence comparison

Geir Egil Hauge geirha at ifi.uio.no
Mon May 13 04:46:54 EST 1991

Special-purpose hardware for fast comparison of DNA and/or protein sequences
I am interested in knowing more about ongoing and finished projects
developing special-purpose hardware for fast comparison of DNA and/or 
protein sequences. 

For example: Have someone constructed a chip or hardware algorithm that
compute optimal alignment score? (maximizing the similarity score or 
minimizing the difference score). 

What about the chip from Applied Biosystems that was mentioned in an article 
by Roberts L.:

"It took 1 day on a supercomputer and 10 days on a VAX. With the new tecnology 
it took 10 minutes". (Roberts 1989).

Is this chip for sale now? Are there any other articles describing this chip? 

What about Motorola, Intel, etc.. Do they have some similar chips for sale 
now or in the near future?

For example: Promixity Technology has manufactured a chip, the "PF474c String 
Comparison Co-processor". (Olsen 1988). But this chip don't seem to be useful 
in computing optimal alignment score. 

Mukhopadhyay, A. has developed interesting hardware algorithms for 
string processing. (Mukhopadhyay 1980).

Mukherjee, A. has solved the LCS (Longest common subsequence) problem in 
hardware. (Mukherjee 1989).
There an interesting CMOS VLSI dynamic time warp processor chip described in 
"Principles of CMOS VLSI Design, A System Perspective". (Weste et al. 1988).
This chip uses an algorithm that in some way looks similar to the optimal 
alignment problem, but do not use a "cost-table" for indels and substitutions. 
Instead it use a difference term. 

If you know about chips or hardware algorithms etc. for the optimal 
alignment score problem, or related problems, then please give some
information to this BIOSCI news group. And please use references.
- I have seen so much interesting material in this news group and
other BIOSCI newsgroups, but references were not given, so its 
difficult to search for more information.

Geir Egil Hauge

 Mukherjee, A., "Hardware algorithms for determining similarity between 2 
   strings", IEEE Transactions on computers 38(4) 600-603 (1989). 
 Mukhopadhyay, A., "Hardware algorithms for string processing", IEEE 
   international conference on circuits and computers ICCC 80
   pp 508-511 (1980). 
 Olsen, M., "Theory and applications of inexact pattern matching:
   A discussion of the PF474 string co-processor", Computers and the 
   Humanities Vol.22, no.3, pp 203-215 (1988).
 Roberts, L., "New chip may speed genome analysis",
   Science 244: 655-656 (1989).
 Weste N., Eshraghian K., "Principles of CMOS VLSI Design, A System 
   Perspective", 1988, Addison-Wesly.

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