Spectrogram analysis of genomes

DOI10.1155/S1110865704310048MaRDI QIDQ1773686zbMATH OpenOpenAlexWikidataFDO

Authors David Sussillo, Anshul Kundaje, Dimitris Anastassiou

Publication date 3 May 2005

Published in EURASIP Journal on Applied Signal Processing (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1155/s1110865704310048

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Protein sequences, DNA sequences (92D20)

Review text

Summary: We performed frequency-domain analysis in the genomes of various organisms using tricolor spectrograms, identifying several types of distinct visual patterns characterizing specific DNA regions. We relate patterns and their frequency characteristics to the sequence characteristics of the DNA. At times, the spectrogram patterns could be related to the structure of the corresponding protein regions by using various public databases such as GenBank. Some patterns are explained from the biological nature of the corresponding regions, which relate to chromosome structure and protein coding, and some patterns have yet unknown biological significance. We found biologically meaningful patterns, on the scale of millions of base pairs, to a few hundred base pairs. Chromosome-wide patterns include periodicities ranging from 2 to 300. The color of the spectrogram depends on the nucleotide content at specific frequencies, and therefore can be used as a local indicator of CG content and other measures of relative base content. Several smaller-scale patterns were found to represent different types of domains made up of various tandem repeats.

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Cited in

(7)

• Chromosome-specific spatial periodicities in gene expression revealed by spectral analysis
• Large-scale chromosome folding versus genomic DNA sequences: a discrete double Fourier transform technique
• Spectral concepts in genome informational analysis
• The role of signal processing concepts in genomics and proteomics
• Biosequence Time–Frequency Processing: Pathogen Detection and Identification
• The formation characteristics of enterobacterial repetitive intergenic consensus (ERIC)-PCR patterns in genomes containing ERIC elements
• Information capacity of nucleotide sequences and its applications

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