Complexity: an internet resource for analysis of DNA sequence complexity
1 Institute of Mathematics SB RAS, prosp. Koptyuga 4, Novosibirsk, 630090 Russia and 2 Institute of Cytology and Genetics SB RAS, Lavrentieva Avenue 10, Novosibirsk, 630090 Russia
* To whom correspondence should be addressed. Tel.: +7 3832 333869; Fax: +7 3832 332598; Email: orlov{at}bionet.nsc.ru
Correspondence may also be addressed to V. N. Potapov. Email: vpotapov{at}math.nsc.ru
The authors wish it to be known that, in their opinion, both authors should be regarded as joint First Authors
Received February 14, 2004; Revised April 20, 2004; Accepted April 29, 2004
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.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.