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                       |
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