复杂性：一个用于分析DNA序列复杂性的互联网资源。
Complexity: an internet resource for analysis of DNA sequence complexity.
作者信息
Orlov Y L, Potapov V N
机构信息
Institute of Mathematics SB RAS, prosp. Koptyuga 4, Novosibirsk, 630090 Russia.
出版信息
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W628-33. doi: 10.1093/nar/gkh466.
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.
摘要
寻找低复杂度的DNA区域是现代全基因组结构分析的关键任务之一。低复杂度可能由核苷酸含量的强烈不均衡（偏向性组成）、串联或分散重复序列、回文-发夹结构以及所有这些因素的组合所导致。文本复杂度的几种数值度量方法，包括组合和语言学方法，以及使用改进的莱姆佩尔-齐夫算法进行的复杂度估计，已在一个名为“Complexity”的软件工具（http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/）中实现。该软件能让用户在长序列（如完整的细菌基因组或真核染色体）中搜索低复杂度区域。此外，它还能估计比对序列组的复杂度。
相似文献
1
Complexity: an internet resource for analysis of DNA sequence complexity.复杂性：一个用于分析DNA序列复杂性的互联网资源。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W628-33. doi: 10.1093/nar/gkh466.
2
Statistical measures of the structure of genomic sequences: entropy, complexity, and position information.基因组序列结构的统计度量：熵、复杂度和位置信息。
J Bioinform Comput Biol. 2006 Apr;4(2):523-36. doi: 10.1142/s0219720006001801.
3
CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.CRASP：一个用于分析蛋白质序列多序列比对中协同替换的程序。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W64-8. doi: 10.1093/nar/gkh451.
4
SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition.SITECON：一种用于检测转录因子结合位点比对中保守构象和物理化学性质以及用于位点识别的工具。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W208-12. doi: 10.1093/nar/gkh474.
5
Construction of stochastic context trees for genetic texts.用于基因文本的随机上下文树构建。
In Silico Biol. 2002;2(3):233-47.
6
RECON: a program for prediction of nucleosome formation potential.RECON：一种用于预测核小体形成潜力的程序。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W346-9. doi: 10.1093/nar/gkh482.
7
Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences.Deltarho-web，一种用于评估单个核酸序列组成相似性的在线工具。
Bioinformatics. 2005 Jul 1;21(13):3053-5. doi: 10.1093/bioinformatics/bti460. Epub 2005 Apr 26.
8
Investigating extended regulatory regions of genomic DNA sequences.研究基因组DNA序列的扩展调控区域。
Bioinformatics. 1999 Jul-Aug;15(7-8):644-53. doi: 10.1093/bioinformatics/15.7.644.
9
MultiPipMaker: comparative alignment server for multiple DNA sequences.MultiPipMaker：用于多个DNA序列的比较比对服务器。
Curr Protoc Bioinformatics. 2005 Apr;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s9.
10
MATCH: A tool for searching transcription factor binding sites in DNA sequences.MATCH：一种用于在DNA序列中搜索转录因子结合位点的工具。
Nucleic Acids Res. 2003 Jul 1;31(13):3576-9. doi: 10.1093/nar/gkg585.
引用本文的文献
1
Tutorial: guidelines for quality filtering of whole-exome and whole-genome sequencing data for population-scale association analyses.教程：用于群体规模关联分析的全外显子组和全基因组测序数据质量过滤指南
Nat Protoc. 2025 Mar 28. doi: 10.1038/s41596-025-01169-1.
2
The rate and spectrum of new mutations in mice inferred by long-read sequencing.通过长读长测序推断的小鼠新突变率和谱。
Genome Res. 2025 Jan 22;35(1):43-54. doi: 10.1101/gr.279982.124.
3
AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data.AlcoR：生物数据中低复杂度区域的无比对模拟、映射和可视化。
Gigascience. 2022 Dec 28;12. doi: 10.1093/gigascience/giad101. Epub 2023 Dec 13.
4
Bioinformatics tools for the sequence complexity estimates.用于序列复杂性估计的生物信息学工具。
Biophys Rev. 2023 Sep 15;15(5):1367-1378. doi: 10.1007/s12551-023-01140-y. eCollection 2023 Oct.
5
MLR-OOD: A Markov Chain Based Likelihood Ratio Method for Out-Of-Distribution Detection of Genomic Sequences.MLR-OOD：基于马尔可夫链的基因组序列分布外检测似然比方法。
J Mol Biol. 2022 Aug 15;434(15):167586. doi: 10.1016/j.jmb.2022.167586. Epub 2022 Apr 12.
6
Basecalling Using Joint Raw and Event Nanopore Data Sequence-to-Sequence Processing.使用联合原始和事件纳米孔数据序列到序列处理进行碱基调用。
Sensors (Basel). 2022 Mar 15;22(6):2275. doi: 10.3390/s22062275.
7
Non-linear Methods Predominant in Fetal Heart Rate Analysis: A Systematic Review.胎儿心率分析中非线性方法占主导地位：一项系统综述。
Front Med (Lausanne). 2021 Nov 30;8:661226. doi: 10.3389/fmed.2021.661226. eCollection 2021.
8
Uncovering patterns of the evolution of genomic sequence entropy and complexity.揭示基因组序列熵和复杂度演化的模式。
Mol Genet Genomics. 2021 Mar;296(2):289-298. doi: 10.1007/s00438-020-01729-y. Epub 2020 Oct 21.
9
A complexity-based measure and its application to phylogenetic analysis.一种基于复杂性的度量及其在系统发育分析中的应用。
J Math Chem. 2009;46(4):1149-1157. doi: 10.1007/s10910-008-9511-3. Epub 2008 Dec 9.
10
Ultra-fast genome comparison for large-scale genomic experiments.用于大规模基因组实验的超快速基因组比较。
Sci Rep. 2019 Jul 16;9(1):10274. doi: 10.1038/s41598-019-46773-w.
本文引用的文献
1
Discovering simple regions in biological sequences associated with scoring schemes.
J Comput Biol. 2003;10(2):171-85. doi: 10.1089/106652703321825955.
2
Construction of stochastic context trees for genetic texts.用于基因文本的随机上下文树构建。
In Silico Biol. 2002;2(3):233-47.
3
Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity.导致人类遗传疾病的插入缺失的荟萃分析：诱变机制及局部DNA序列复杂性的作用
Hum Mutat. 2003 Jan;21(1):28-44. doi: 10.1002/humu.10146.
4
Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects.基因组大小与简单序列重复序列的积累：来自基因组测序项目新数据的启示
Genetica. 2002 May;115(1):93-103. doi: 10.1023/a:1016028332006.
5
Sequence complexity profiles of prokaryotic genomic sequences: a fast algorithm for calculating linguistic complexity.原核生物基因组序列的序列复杂性概况：一种计算语言复杂性的快速算法。
Bioinformatics. 2002 May;18(5):679-88. doi: 10.1093/bioinformatics/18.5.679.
6
Detecting cryptically simple protein sequences using the SIMPLE algorithm.使用SIMPLE算法检测隐蔽的简单蛋白质序列。
Bioinformatics. 2002 May;18(5):672-8. doi: 10.1093/bioinformatics/18.5.672.
7
Entropy and complexity of finite sequences as fluctuating quantities.作为波动量的有限序列的熵与复杂性。
Biosystems. 2002 Jan;64(1-3):23-32. doi: 10.1016/s0303-2647(01)00171-x.
8
Discovering patterns in Plasmodium falciparum genomic DNA.发现恶性疟原虫基因组DNA中的模式。
Mol Biochem Parasitol. 2001 Dec;118(2):175-86. doi: 10.1016/s0166-6851(01)00388-7.
9
SpliceDB: database of canonical and non-canonical mammalian splice sites.SpliceDB：哺乳动物标准和非标准剪接位点数据库。
Nucleic Acids Res. 2001 Jan 1;29(1):255-9. doi: 10.1093/nar/29.1.255.
10
A Compression Algorithm for DNA Sequences and Its Applications in Genome Comparison.一种用于DNA序列的压缩算法及其在基因组比较中的应用。
Genome Inform Ser Workshop Genome Inform. 1999;10:51-61.
Zotero 插件