Hi all,
I would like you to point me out some good articles regarding the use of algorithms to mask low complexity regions in DNA strings. My purpose is to clean up sequences in order to search for putative TFBS (by the way, I an not so sure this is a good idea, but this is another topic), so I also welcome literature about the use of such algorithms in the TFBS search. In particular, I would like you to explain me how did you organize your search in Pubmed et similia, as I failed to find something by my self.
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written
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Anima Mundi
2 answers
Hi,
programs to screen and mask low complexity regions:
- Repbase: is a collection of repetitive DNA elements broken up along organismal lines
- RepeatMasker: screens DNA sequences for interspersed repeats and low complexity DNA sequences. It can be used to mask regions of low complexity. It can also be used to identify and mask-out contaminating sequences as well
- DUST: A fast and symmetric DUST implementation to mask low-complexity DNA sequences.
- SEG: the protein counterpart for filtering low complexity regions in amino acid sequences
This link (DNA Patterns & Motifs) should help you find a right tool for further analysis.
A helpful article: Discovering Sequence Motifs by Timothy L. Bailey
I hope this helps.
I did get some good results with TANTAN: http://nar.oxfordjournals.org/content/early/2010/11/24/nar.gkq1212.full
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I rather thought Repeatmasker was still pretty much the accepted way to do this: http://www.repeatmasker.org/
Anima, I think this "I would like you to explain me how did you organize your search in Pubmed et similia, as I failed to find something by my self." should be a separate question.