scholarly journals Identification of Protein Coding Regions in the Eukaryotic DNA Sequences Based on Marple Algorithm and Wavelet Packets Transform

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Guangchen Liu ◽  
Yihui Luan
Keyword(s):  
Dna Sequences ◽  
Structure Prediction ◽  
Critical Role ◽  
Wavelet Packets ◽  
Protein Coding ◽  
Gene Structure Prediction ◽  
Coding Regions ◽  
Eukaryotic Gene ◽  
Benchmark Datasets ◽  
Eukaryotic Dna

The identification of protein coding regions (exons) plays a critical role in eukaryotic gene structure prediction. Many techniques have been introduced for discriminating between the exons and the introns in the eukaryotic DNA sequences, such as the discrete Fourier transform (DFT) based techniques, but these DFT-based methods rapidly lose their effectiveness in the case of short DNA sequences. In this paper, a novel integrated algorithm based on autoregressive spectrum analysis and wavelet packets transform is presented to improve the efficiency and accuracy of the coding regions identification. The experimental results show that the new algorithm outperforms the conventional DFT-based approaches in improving the prediction accuracy of protein coding regions distinctly by testing GENSCAN65, HMR195, and BG570 benchmark datasets.

scholarly journals A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Type Specimens ◽  
African Species ◽  
Protein Coding ◽  
Coding Regions ◽  
As Species ◽  
Close Relatives ◽  
Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]). 

scholarly journals Recognition of protein coding regions in DNA sequences

1982 ◽  
Vol 10 (17) ◽  
pp. 5303-5318 ◽  
Author(s):  
James W. Fickett
Keyword(s):  
Dna Sequences ◽  
Protein Coding ◽  
Coding Regions

scholarly journals Estimation of protein-coding regions in numerical DNA sequences using Variable Length Window method based on 3-D Z-curve

2017 ◽  
Vol 13 (4) ◽  
pp. 63-78
Author(s):  
حمیدرضا صابرکاری ◽  
موسی شمسی ◽  
Hossein صداقی ◽  
◽  
◽  
...  
Keyword(s):  
Dna Sequences ◽  
Variable Length ◽  
Protein Coding ◽  
Coding Regions ◽  
Window Method ◽  
Z Curve

scholarly journals A Novel Approach For Identification Of Exon Locations In DNA Sequences Using GLC Window

2021 ◽  
Vol 15 ◽  
pp. 47-60
Author(s):  
P. Kamala Kumari ◽  
J.B. Seventline
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Side Lobe ◽  
Window Function ◽  
Protein Coding ◽  
C Elegans ◽  
Novel Approach ◽  
Benchmark Datasets ◽  
Window Approach ◽  
Sensitivity Specificity

The application of signal processing techniques for identification of exons in Deoxyribonucleic acid (DNA) sequence is a challenging task. The objective of this paper is to introduce a combinational window approach for locating exons in DNA sequence. In contrast to the traditional single window function for evaluation of short time Fourier transform (STFT), this work proposes a novel method for evaluating STFT coefficients using a combinational window function comprising of Gaussian, Lanczos and Chebyshev (GLC) windows. The chosen combinational window GLC has the highest relative side lobe attenuation values compared to other window functions introduced by various researchers. The proposed algorithm incorporates GLC window function for evaluating STFT coefficients and in the design of FIR bandpass filter. Simulation results revealed its effectiveness in improving the evaluation parameters like Sensitivity, Specificity, Accuracy, Area under curve (AUC), Discrimination Measure (DM). Furthermore, the proposed algorithm has been applied successfully to some universal benchmark datasets like C. elegans, Homosapiens, etc., The proposed method has shown to be an efficient approach for the prediction of protein coding regions compared to other existing methods. All the simulations are done using the MATLAB 2016a.

Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity

2003 ◽  
Vol 33 (11) ◽  
pp. 2245-2251 ◽  
Author(s):  
Brigid Stirling ◽  
Zamin Koo Yang ◽  
Lee E Gunter ◽  
Gerald A Tuskan ◽  
H D Bradshaw Jr.
Keyword(s):  
Sequence Analysis ◽  
Dna Sequences ◽  
Artificial Chromosome ◽  
Comparative Sequence Analysis ◽  
Complete Sequence ◽  
Arabidopsis Genome ◽  
Protein Coding ◽  
Coding Regions ◽  
Bac Clones ◽  
Populus Genome

More than 300 kb of DNA sequence from five Populus bacterial artificial chromosome (BAC) clones was compared with the complete sequence of the Arabidopsis genome to search for collinearity between the genomes of these two plant genera. Approximately 27% of the DNA sequences from the Populus genome were homologous to protein-coding regions in the Arabidopsis genome. BLAST scores and synteny were used to infer orthologous relationships between the Populus and Arabidopsis homologs. The probability that any pair of genes on a single Populus BAC will have orthologs on the same Arabidopsis chromosome is 46%–58%, substantially greater than the 20% expectation if there is no conservation of synteny between the Populus and Arabidopsis genomes. Likewise, the probability that any pair of genes on a single Populus BAC will have orthologs on a single Arabidopsis BAC is 19%–25%, much higher than the 0.1% expected if the orthologs are randomly distributed. These results provide evidence for substantial "pockets" of conserved microcollinearity between regions of the Populus and Arabidopsis genomes as well as for conservation of synteny even when local gene collinearity is not preserved during genome evolution.

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