Sequence comparison and classification of beet luteovirus isolates

1995 ◽  
Vol 140 (12) ◽  
pp. 2183-2200 ◽  
Author(s):  
J. R. de Miranda ◽  
M. Stevens ◽  
E. de Bruyne ◽  
H. G. Smith ◽  
C. Bird ◽  
...  
Keyword(s):  
Sequence Comparison

scholarly journals PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses

Viruses ◽  
2012 ◽  
Vol 4 (8) ◽  
pp. 1318-1327 ◽  
Author(s):  
Yiming Bao ◽  
Vyacheslav Chetvernin ◽  
Tatiana Tatusova
Keyword(s):  
Sequence Comparison ◽  
Pairwise Sequence Comparison

scholarly journals A sequential development towards a unified approach to protein sequence comparison based on classified groups of amino acids

2018 ◽  
Vol 7 (2) ◽  
pp. 678
Author(s):  
Soumen Ghosh ◽  
Jayanta Pal ◽  
Bansibadan Maji ◽  
Dilip Kumar Bhattacharya
Keyword(s):  
Amino Acids ◽  
Protein Sequence ◽  
Sequence Comparison ◽  
Protein Sequences ◽  
Group Classification ◽  
Unified Approach ◽  
The Unified Method ◽  
Protein Sequence Comparison ◽  
Unified Method

The methods of comparison of protein sequences based on different classified groups of amino acids add a significant contribution to the literature of protein sequence comparison. But the methods vary with choice of different classified groups. Therefore, the purpose of the paper is to develop a unified approach towards the analysis of protein sequence comparison based on classification of amino acids in different groups of different cardinality. The paper considers 4 group classification, 5 group classification and 6 group classifications of amino acids, and in each case it applies the unified method for comparing two types of protein sequences, viz., 9 proteins of ND5 category and 50 Corona virus Spike Proteins. The results agree with those, which were obtained earlier by other methods based on classified groups of amino acids. An-yway it is found that the present unified formula is relatively simpler and fundamentally different from the earlier ones. Further, it can be applied conveniently in comparison of protein sequences based on all different types of classified groups of amino acids.

scholarly journals Sequence comparison and classification of beet luteovirus isolates

1996 ◽  
Vol 141 (5) ◽  
pp. 985-985
Author(s):  
J. R. de Miranda
Keyword(s):  
Sequence Comparison

Cloning and characterization of ribosomal RNA genes from Opisthorchis viverrini

Parasitology ◽  
1992 ◽  
Vol 104 (2) ◽  
pp. 323-329 ◽  
Author(s):  
S. Korbsrisate ◽  
S. Mongkolsuk ◽  
J. R. Haynes ◽  
Q. Wong ◽  
S. Sirisinha
Keyword(s):  
Ribosomal Rna ◽  
Sequence Comparison ◽  
Genomic Dna ◽  
Opisthorchis Viverrini ◽  
Lsu Rdna ◽  
Rrna Gene ◽  
Phylogenetic Classification ◽  
Lsu Rrna ◽  
Spacer Dna

SUMMARYThe ribosomal DNA (rDNA) unit of the liver fluke Opisthorchis viverrini has been cloned and characterized. The results demonstrated that the total length of this unit is approximately 13 kb, containing 4·2 kb of large subunit (LSU) rDNA, 2·0 kb of small subunit (SSU) rDNA, 1·0 kb of transcribed spacer DNA and 5·8 kb of non-transcribed + external transcribed spacer DNA. Examination of the non-transcribed spacer region between different rDNA units showed variation in the restriction sites rather than in the length. Judging from hybridization of the rDNA plasmid to the restriction endonuclease digest of genomic DNA, rDNA units represent 6·1% of the total genomic DNA. At the RNA level, the LSU rRNA of O. viverrini and Fasciola gigantica contained a hidden break. The molecule consisted of two fragments co-migrating with a SSU rRNA, when electrophoresis was carried out under denaturing conditions. Ribosomal RNA sequence comparison has been previously used to determine phylogenetic classification of parasitic organisms. The sequence of 381 nucleotides at the 5′ terminus of the LSU rRNA gene was determined and compared with those from species previously reported by other investigators. Phylogenetic classification of O. viverrini, as determined by rRNA gene sequence comparison, is comparable with the conventional taxonomic classification.

scholarly journals Phylogenetic relationships between genera Dorcadion, Lamia, Morimus, Herophila and some other Lamiinae (Coleoptera: Cerambycidae) based on chromosome and CO1 gene sequence comparison

2019 ◽  
Vol 110 (3) ◽  
pp. 321-327
Author(s):  
Themis Giannoulis ◽  
Anne-Marie Dutrillaux ◽  
Constantina Sarri ◽  
Zissis Mamuris ◽  
Bernard Dutrillaux
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Comparison ◽  
Gene Sequence ◽  
Cytogenetic Study ◽  
Hybrid Origin ◽  
Systematic Classification ◽  
Phylogenetic Classification ◽  
Distant Relationship ◽  
In Captivity

AbstractA dual molecular and cytogenetic study was performed with the aim to improve the controversial systematic classification of some species of Lamiinae (Coleoptera: Cerambycidae). The karyotypes of species belonging to genera Morimus, Herophila, Dorcadion, Neodorcadion and Lamia share a number of characters, which differentiate them from other species, belonging to genera Phytoecia, Parmena and Monochamus. The karyotypes of the last three species comprise 20 chromosomes, mostly metacentric or sub-metacentric, as in the presumed Cerambycidae ancestors. The karyotypes of the former species share many characters derived from the Lamiinae ancestors by a number of chromosome fissions and inversions indicating their monophyly. Comparisons of the CO1 gene sequence also show the monophyly of Morimus, Lamia, Herophila and Dorcadion and their distant relationship with others. These convergent results allow us to propose a phylogenetic classification of these genera, which places the monospecific genus Lamia close to Dorcadion, clearly separates Dorcadion and Neodorcadion and places Herophila closer to Morimus than to Dorcadion/Lamia. The genus Morimus is the most derived. CO1 mutations loosely separate the forms M. asper and M. funereus, which have similar karyotypes and behaviour and copulate in captivity. The form M. ganglebaueri may have a funereus X asper hybrid origin.

scholarly journals Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1476
Author(s):  
Lester J. Perez ◽  
Gavin A. Cloherty ◽  
Michael G. Berg
Keyword(s):  
Genetic Diversity ◽  
Sequence Comparison ◽  
Complete Resolution ◽  
Pairwise Distance ◽  
Pairwise Sequence Comparison ◽  
Double Stranded Rna ◽  
Phylogenetic Marker ◽  
High Degree ◽  
Phylogenetic Noise

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

Note on the spectral classification of carbon stars in the photographic infrared region

1966 ◽  
Vol 24 ◽  
pp. 21-23
Author(s):  
Y. Fujita
Keyword(s):  
Infrared Region ◽  
Spectral Classification ◽  
Carbon Stars

We have investigated the spectrograms (dispersion: 8Å/mm) in the photographic infrared region fromλ7500 toλ9000 of some carbon stars obtained by the coudé spectrograph of the 74-inch reflector attached to the Okayama Astrophysical Observatory. The names of the stars investigated are listed in Table 1.

Diagnostic Value of Electron Microscopy in Soft Tissue Tumors

1970 ◽  
Vol 28 ◽  
pp. 220-221
Author(s):  
Gerald Fine ◽  
Azorides R. Morales
Keyword(s):  
Cardiac Myxoma ◽  
Osteogenic Sarcoma ◽  
Diagnostic Value ◽  
Soft Tissue Tumors ◽  
Amelanotic Melanoma ◽  
Growth Patterns ◽  
Light Microscopic Level ◽  
Mesenchymal Tumors ◽  
Good Agreement

For years the separation of carcinoma and sarcoma and the subclassification of sarcomas has been based on the appearance of the tumor cells and their microscopic growth pattern and information derived from certain histochemical and special stains. Although this method of study has produced good agreement among pathologists in the separation of carcinoma from sarcoma, it has given less uniform results in the subclassification of sarcomas. There remain examples of neoplasms of different histogenesis, the classification of which is questionable because of similar cytologic and growth patterns at the light microscopic level; i.e. amelanotic melanoma versus carcinoma and occasionally sarcoma, sarcomas with an epithelial pattern of growth simulating carcinoma, histologically similar mesenchymal tumors of different histogenesis (histiocytoma versus rhabdomyosarcoma, lytic osteogenic sarcoma versus rhabdomyosarcoma), and myxomatous mesenchymal tumors of diverse histogenesis (myxoid rhabdo and liposarcomas, cardiac myxoma, myxoid neurofibroma, etc.)

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