New statistical approach to discriminate between protein coding and non-coding regions in DNA sequences and its evaluation

1986 ◽  
Vol 120 (2) ◽  
pp. 223-236 ◽  
Author(s):  
Christian J. Michel
Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN

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]). 


Author(s):  
В.А. Кутыркин ◽  
V.A. Kutyrkin

Structural-statistical characteristics of the coding DNA sequences (CDSs) from human genome are investigated in the frame of spectral-statistical approach (the 2S-approach). Properties of 3-regularity and latent profile periodicity are among of such the characteristics. Special meaning and intrinsic existence of these properties are confirmed by researching the binary recoded CDSs. The only one kind of singular recoding, that identifies complementary nucleotides, serves to persistence of the original CDSs characteristics. Usage of nonsingular binary recoding proves a statement that latent triplet periodicity in the CDSs of human genome belongs to earlier unknown type called as profile periodicity.


1982 ◽  
Vol 10 (17) ◽  
pp. 5303-5318 ◽  
Author(s):  
James W. Fickett

2017 ◽  
Vol 13 (4) ◽  
pp. 63-78
Author(s):  
حمیدرضا صابرکاری ◽  
موسی شمسی ◽  
Hossein صداقی ◽  
◽  
◽  
...  

2003 ◽  
Vol 33 (11) ◽  
pp. 2245-2251 ◽  
Author(s):  
Brigid Stirling ◽  
Zamin Koo Yang ◽  
Lee E Gunter ◽  
Gerald A Tuskan ◽  
H D Bradshaw Jr.

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.


1995 ◽  
Vol 06 (01) ◽  
pp. 31-42 ◽  
Author(s):  
N. TOLSTRUP

Optimal Brain Damage (OBD) and Optimal Brain Surgeon (OBS) represent two popular pruning procedures; however, pruning large networks trained on voluminous data sets using these methods easily becomes intractable. We present a number of approximations and discuss practical issues in real-world pruning, and use as an example a network trained to predict protein coding regions in DNA sequences. The efficiency of OBS on large networks is compared to OBD, and it turns out that OBD is preferable to OBS, since more weights can be removed using less computational effort.


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