internal repeats

Fredj Tekaia tekaia at pasteur.fr
Fri May 14 09:11:34 EST 1993


In article <1survlINNdfl at phage.cshl.org> wli at phage.cshl.org ( CSHL) writes:
>
>i'm looking for a C code which lists *all* internal repeats
>in a sequence. no restriction on the repeating unit size,
>the distance between the repeat units, or anything. this
>list has to be complete.
>
>is it a trivial task or a tricky one? i'm new to this topic, 
>so i have no idea. any pointer is appreciated...( public
>domain code, reference... or your own program-- i don't need
>a complete code, only the subroutine dealing with this task
>would be fine).

 The solution suggested by Gonnet is beautiful! you might also have
a look in the SAPS (Statistical Analysis of Protein Sequences)
programm (V. Brendel volker at gnomic.stabford.edu).
Repetitive structures, among other compositional and
distribution analysis, are investigated: separated, tandem and
periodic repeats. Nevertheless there is a restriction on the block
length of contiguous exact matches: it should exceed a given value, at
least 4.

Fredj Tekaia

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