Complexity: an internet resource for analysis of DNA sequence complexity

The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures,...

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Bibliographic Details
Published in:Nucleic acids research 2004-07, Vol.32 (suppl-2), p.W628-W633
Main Authors: Orlov, Y. L., Potapov, V. N.
Format: Article
Language:English
Subjects:
Algorithms
Chromosomes
Genome, Bacterial
Internet
Sequence Alignment
Sequence Analysis, DNA
Software
User-Computer Interface
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Summary:The search for DNA regions with low complexity is one of the pivotal tasks of modern structural analysis of complete genomes. The low complexity may be preconditioned by strong inequality in nucleotide content (biased composition), by tandem or dispersed repeats or by palindrome-hairpin structures, as well as by a combination of all these factors. Several numerical measures of textual complexity, including combinatorial and linguistic ones, together with complexity estimation using a modified Lempel–Ziv algorithm, have been implemented in a software tool called ‘Complexity’ (http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/). The software enables a user to search for low-complexity regions in long sequences, e.g. complete bacterial genomes or eukaryotic chromosomes. In addition, it estimates the complexity of groups of aligned sequences.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkh466