Literature DB >> 15215465

Complexity: an internet resource for analysis of DNA sequence complexity.

Y L Orlov1, V N Potapov.   

Abstract

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.

Mesh：

Year:  2004        PMID： 15215465      PMCID： PMC441604          DOI： 10.1093/nar/gkh466

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  16 in total

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Journal:  Biosystems       Date:  2002-01       Impact factor: 1.973

4.  Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects.

Authors:  John M Hancock
Journal:  Genetica       Date:  2002-05       Impact factor: 1.082

5.  Detecting cryptically simple protein sequences using the SIMPLE algorithm.

Authors:  M Mar Albà; Roman A Laskowski; John M Hancock
Journal:  Bioinformatics       Date:  2002-05       Impact factor: 6.937

6.  Construction of stochastic context trees for genetic texts.

Authors:  Yury L Orlov; Vladimir P Filippov; Vladimir N Potapov; Nikolay A Kolchanov
Journal:  In Silico Biol       Date:  2002

7.  Discovering simple regions in biological sequences associated with scoring schemes.

Authors:  Honghui Wan; Lugang Li; Scott Federhen; John C Wootton
Journal:  J Comput Biol       Date:  2003       Impact factor: 1.479

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Journal:  Mol Biol (Mosk)       Date:  1991 May-Jun

9.  Characteristic enrichment of DNA repeats in different genomes.

Authors:  R Cox; S M Mirkin
Journal:  Proc Natl Acad Sci U S A       Date:  1997-05-13       Impact factor: 11.205

10.  Discovering patterns in Plasmodium falciparum genomic DNA.

Authors:  L Stern; L Allison; R L Coppel; T I Dix
Journal:  Mol Biochem Parasitol       Date:  2001-12       Impact factor: 1.759
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  20 in total

1.  Complexity analysis of the cerebrospinal fluid pulse waveform during infusion studies.

Authors:  David Santamarta; Roberto Hornero; Daniel Abásolo; Milton Martínez-Madrigal; Javier Fernández; Jose García-Cosamalón
Journal:  Childs Nerv Syst       Date:  2010-08-03       Impact factor: 1.475

2.  Nonlinear dynamical analysis of carbachol induced hippocampal oscillations in mice.

Authors:  Metin Akay; Kui Wang; Yasemin M Akay; Andrei Dragomir; Jie Wu
Journal:  Acta Pharmacol Sin       Date:  2009-06       Impact factor: 6.150

3.  Ultra-fast genome comparison for large-scale genomic experiments.

Authors:  Esteban Pérez-Wohlfeil; Sergio Diaz-Del-Pino; Oswaldo Trelles
Journal:  Sci Rep       Date:  2019-07-16       Impact factor: 4.379

4.  Uncovering patterns of the evolution of genomic sequence entropy and complexity.

Authors:  Rafael Plana Simões; Ivan Rodrigo Wolf; Bruno Afonso Correa; Guilherme Targino Valente
Journal:  Mol Genet Genomics       Date:  2020-10-21       Impact factor: 3.291

5.  Realistic artificial DNA sequences as negative controls for computational genomics.

Authors:  Juan Caballero; Arian F A Smit; Leroy Hood; Gustavo Glusman
Journal:  Nucleic Acids Res       Date:  2014-05-06       Impact factor: 16.971

6.  FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut.

Authors:  Stephan Nielen; Fernando Campos-Fonseca; Soraya Leal-Bertioli; Patricia Guimarães; Guillermo Seijo; Christopher Town; Roberto Arrial; David Bertioli
Journal:  Chromosome Res       Date:  2010-02-02       Impact factor: 5.239

7.  Complexity analysis of the fetal heart rate variability: early identification of severe intrauterine growth-restricted fetuses.

Authors:  Manuela Ferrario; Maria G Signorini; Giovanni Magenes
Journal:  Med Biol Eng Comput       Date:  2009-06-13       Impact factor: 2.602

8.  Complexity of VTA DA neural activities in response to PFC transection in nicotine treated rats.

Authors:  Ting Y Chen; Die Zhang; Andrei Dragomir; Yasemin M Akay; Metin Akay
Journal:  J Neuroeng Rehabil       Date:  2011-02-27       Impact factor: 4.262

9.  Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

Authors:  Irina Abnizova; Rene te Boekhorst; Klaudia Walter; Walter R Gilks
Journal:  BMC Bioinformatics       Date:  2005-04-27       Impact factor: 3.169

10.  Evolutionary hierarchies of conserved blocks in 5'-noncoding sequences of dicot rbcS genes.

Authors:  Katie E Weeks; Nadia A Chuzhanova; Iain S Donnison; Ian M Scott
Journal:  BMC Evol Biol       Date:  2007-04-02       Impact factor: 3.260
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