Palindromes, homopolymers and simple repeats .

Description

This series contains features that are directly computed from the genome sequence with ad hoc scripts, including short palindromes, homopolymers and simple repeats. Some of these features appear to be enriched or depleted in certains regions. For instance, palindromes are enriched in the regulatory regions of certain species. Simple repeats tend to be depleted in conserved non-coding regions.

Source

Samples

From D. melanogaster (Aug 2014 BDGP Rel6 + ISO1 MT/dm6).

Sequence-derived:

Filename Description Feature GEO-ID
1 wwwwww.sga W-hexamers 6W -
2 ssssss.sga S-hexamers 6S -
3 rrrrrr.sga R(+)/Y(-)-hexamers 6R -
4 mmmmmm.sga M(+)/K(-)-hexamers 6M -
5 aaaaaa.sga hexa-homopolymers (aaaaaa) aaaaaa -
6 ababab.sga 3x2-repeats (ababab) ababab -
7 abcabc.sga 2x3-repeats (abcabc) abcabc -
8 abcxyz.sga hexa-palindromes (abcxyz) abcxyz -
9 abcNxyz.sga hepta-palindromes (abcNxyz) abcNxyz -

the palrep documentation for hg19 at:

http://ccg.vital-it.ch/mga/hg19/palrep/palrep.html

Last update: 22 Dec 2016