Searching for Palindromes, direct/inverted repeats

Lee F. Kolakowski lfk at eastman1.mit.edu
Tue Oct 1 08:32:42 EST 1991


On 1 Oct 91 02:02:46 GMT,
eesnyder at boulder.Colorado.EDU (Eric E. Snyder) said:
> I am looking for a program that will detect palindromes,
> inverted or direct repeats in a given DNA sequence.  Does
> any one have or know where I could find such a program?

Stadens STuff does this...

nip has a part called 

Structures and repeats menu
 0 = List of menus
30 = Search for hairpin loops
31 = Search for long range inverted repeats
32 = Search for repeats
33 = Search for z dna (total ry,yr)
34 = Search for z dna (runs of ry or yr)
35 = Search for z dna (best phased value)
36 = Search for local similarity or complementarity
? Menu or option number=

This does a pretty good job of searching for repeats.

--

Frank Kolakowski

=======================================================================
|lfk at athena.mit.edu or lfk at eastman1.mit.edu or kolakowski at wccf.mit.edu|
| Lee F. Kolakowski                 M.I.T.                            |
| Dept of Chemistry                 Room 18-506                       |
| 77 Massachusetts Ave.             Cambridge, MA 02139               |
| AT&T:  1-617-253-1866             #include <disclaimer.h>           |
=======================================================================




More information about the Bio-soft mailing list