Shannon Information in Complete Genomes

Chang, Chang-Heng; Hsieh, Li-Ching; Chen, Ta-Yuan; Chen, Hongda; Luo, Liaofu; Lee, Hoong-Chien

doi:10.1142/s0219720005001181

Cited by 25 publications

(22 citation statements)

References 24 publications

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“…Word length is reportedly an important factor influencing the value of Shannon's index67. A high Shannon's index (close to the maximum possible index, i.e., for word length n , the maximum index will be 2n ) depends on the presence of all possible combinations of words in the genome.…”

Section: Resultsmentioning

confidence: 99%

“…Several investigators have examined different aspects of information content of genomes, including Shannon's uncertainty56789 and symmetry1011. For example, Chang and coworkers calculated Shannon's uncertainty index for all the complete prokaryotic and eukaryotic genomes available in 2005.…”

mentioning

confidence: 99%

“…For example, Chang and coworkers calculated Shannon's uncertainty index for all the complete prokaryotic and eukaryotic genomes available in 2005. They found that Shannon's information in complete genomes is greater than that in matching random sequences and they described a coarse-grain model for genome growth and evolution that allows a genome to diverge at any stage during its growth67.…”

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confidence: 99%

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Applying Shannon's information theory to bacterial and phage genomes and metagenomes

Akhter

Bailey

Salamon

et al. 2013

Sci Rep

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All sequence data contain inherent information that can be measured by Shannon's uncertainty theory. Such measurement is valuable in evaluating large data sets, such as metagenomic libraries, to prioritize their analysis and annotation, thus saving computational resources. Here, Shannon's index of complete phage and bacterial genomes was examined. The information content of a genome was found to be highly dependent on the genome length, GC content, and sequence word size. In metagenomic sequences, the amount of information correlated with the number of matches found by comparison to sequence databases. A sequence with more information (higher uncertainty) has a higher probability of being significantly similar to other sequences in the database. Measuring uncertainty may be used for rapid screening for sequences with matches in available database, prioritizing computational resources, and indicating which sequences with no known similarities are likely to be important for more detailed analysis.

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Section: Resultsmentioning

confidence: 99%

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Applying Shannon's information theory to bacterial and phage genomes and metagenomes

Akhter

Bailey

Salamon

et al. 2013

Sci Rep

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“…Although the mechanisms underlying this phenomenon are not fully understood, they are thought to be related to genome and gene duplication, as well as speciation. Such events are expected be more frequent in fish, since the ancestor of today's teleosts seems to have experienced an additional round of genome duplication (Meyer & Schartl, 1999;Postlethwait et al, 2000) and chromosome duplications (Chang et al, 2005) after their ancestor has split from that of the other vertebrates. Duplication of microsatellite loci followed by gene conversion can lead to amplification of non-orthologous loci as proposed (Angers et al, 2002).…”

Section: Discussionmentioning

confidence: 99%

A New Problem with Cross-Species Amplification of Microsatellites: Generation of Non-Homologous Products

Yue¹,

Kovács²,

Orbán³

2010

Zoological Research

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Abstract:Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology. However, microsatellites are not always available for the species to be studied and their isolation could be time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of electromorphs from seven catfish species belonging to three different families (Clariidae, Heteropneustidae and Pimelodidae). A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4 microsatellite loci isolated from the species Clarias batrachus. Two hundred and forty PCR-products representing all 50 electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all species tested, whereas primers for the other two loci produced specific and polymorphic bands from some non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance of size homoplasy will lead to obvious complications in phylogenetic interference, population genetic and evolutionary studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to application of cross-species amplification of microsatellites.

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“…Studies of the 1D histograms of extant complete genomes in contrast to their random counterparts have revealed the existence of universal length in complete genomes that can be explained by a simple universal model for genome growth and evolution 5., 6.. In order to see that an observed feature does not occur in a random sequence, it is desirable to have randomization function built-in.…”

Section: Introductionmentioning

confidence: 99%

SeeDNA: A Visualization Tool for K-String Content of Long DNA Sequences and Their Randomized Counterparts

Shen

Zhang

Lee

et al. 2004

Genomics, Proteomics &Amp; Bioinformatics

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An interactive tool to visualize the K-string composition of long DNA sequences including bacterial complete genomes is described. It is especially useful for exploring short palindromic structures in the sequences. The SeeDNA program runs on Red Hat Linux with GTK+ support. It displays two-dimensional (2D) or one-dimensional (1D) histograms of the K-string distribution of a given sequence and/or its randomized counterpart. It is also capable of showing the difference of K-string distributions between two sequences. The C source code using the GTK+ package is freely available.

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Shannon Information in Complete Genomes

Cited by 25 publications

References 24 publications

Applying Shannon's information theory to bacterial and phage genomes and metagenomes

Applying Shannon's information theory to bacterial and phage genomes and metagenomes

A New Problem with Cross-Species Amplification of Microsatellites: Generation of Non-Homologous Products

SeeDNA: A Visualization Tool for K-String Content of Long DNA Sequences and Their Randomized Counterparts

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