Classification of dsDNA Virus Through Sequence Patterns

Author(s):  
Uddalak Mitra ◽  
Balaram Bhattacharyya
Author(s):  
Rafał Biedrzycki ◽  
Jarosław Arabas

Abstract This paper presents an application of methods from the machine learning domain to solving the task of DNA sequence recognition. We present an algorithm that learns to recognize groups of DNA sequences sharing common features such as sequence functionality. We demonstrate application of the algorithm to find splice sites, i.e., to properly detect donor and acceptor sequences. We compare the results with those of reference methods that have been designed and tuned to detect splice sites. We also show how to use the algorithm to find a human readable model of the IRE (Iron-Responsive Element) and to find IRE sequences. The method, although universal, yields results which are of quality comparable to those obtained by reference methods. In contrast to reference methods, this approach uses models that operate on sequence patterns, which facilitates interpretation of the results by humans.


2009 ◽  
Vol 4 (2) ◽  
pp. 80-83 ◽  
Author(s):  
Alaguraj Veluchamy ◽  
Sujitha Mary ◽  
Vishal Acharya ◽  
Preeti Mehta ◽  
Taru Deva ◽  
...  

Blood ◽  
2012 ◽  
Vol 119 (19) ◽  
pp. 4467-4475 ◽  
Author(s):  
Andreas Agathangelidis ◽  
Nikos Darzentas ◽  
Anastasia Hadzidimitriou ◽  
Xavier Brochet ◽  
Fiona Murray ◽  
...  

Abstract Mounting evidence indicates that grouping of chronic lymphocytic leukemia (CLL) into distinct subsets with stereotyped BCRs is functionally and prognostically relevant. However, several issues need revisiting, including the criteria for identification of BCR stereotypy and its actual frequency as well as the identification of “CLL-biased” features in BCR Ig stereotypes. To this end, we examined 7596 Ig VH (IGHV-IGHD-IGHJ) sequences from 7424 CLL patients, 3 times the size of the largest published series, with an updated version of our purpose-built clustering algorithm. We document that CLL may be subdivided into 2 distinct categories: one with stereotyped and the other with nonstereotyped BCRs, at an approximate ratio of 1:2, and provide evidence suggesting a different ontogeny for these 2 categories. We also show that subset-defining sequence patterns in CLL differ from those underlying BCR stereotypy in other B-cell malignancies. Notably, 19 major subsets contained from 20 to 213 sequences each, collectively accounting for 943 sequences or one-eighth of the cohort. Hence, this compartmentalized examination of VH sequences may pave the way toward a molecular classification of CLL with implications for targeted therapeutic interventions, applicable to a significant number of patients assigned to the same subset.


2018 ◽  
Vol 35 (14) ◽  
pp. 2349-2353 ◽  
Author(s):  
Vikram Alva ◽  
Andrei N Lupas

Abstract Motivation Histones form octameric complexes called nucleosomes, which organize the genomic DNA of eukaryotes into chromatin. Each nucleosome comprises two copies each of the histones H2A, H2B, H3 and H4, which share a common ancestry. Although histones were initially thought to be a eukaryotic innovation, the subsequent identification of archaeal homologs led to the notion that histones emerged before the divergence of archaea and eukaryotes. Results Here, we report the detection and classification of two new groups of histone homologs, which are present in both archaea and bacteria. Proteins in one group consist of two histone subunits welded into single-chain pseudodimers, whereas in the other they resemble eukaryotic core histone subunits and show sequence patterns characteristic of DNA binding. The sequences come from a broad spectrum of deeply-branching lineages, excluding their genesis by horizontal gene transfer. Our results extend the origin of histones to the last universal common ancestor. Supplementary information Supplementary data are available at Bioinformatics online.


1966 ◽  
Vol 24 ◽  
pp. 21-23
Author(s):  
Y. Fujita

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.


Author(s):  
Gerald Fine ◽  
Azorides R. Morales

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.)


Author(s):  
Irving Dardick

With the extensive industrial use of asbestos in this century and the long latent period (20-50 years) between exposure and tumor presentation, the incidence of malignant mesothelioma is now increasing. Thus, surgical pathologists are more frequently faced with the dilemma of differentiating mesothelioma from metastatic adenocarcinoma and spindle-cell sarcoma involving serosal surfaces. Electron microscopy is amodality useful in clarifying this problem.In utilizing ultrastructural features in the diagnosis of mesothelioma, it is essential to appreciate that the classification of this tumor reflects a variety of morphologic forms of differing biologic behavior (Table 1). Furthermore, with the variable histology and degree of differentiation in mesotheliomas it might be expected that the ultrastructure of such tumors also reflects a range of cytological features. Such is the case.


Author(s):  
Paul DeCosta ◽  
Kyugon Cho ◽  
Stephen Shemlon ◽  
Heesung Jun ◽  
Stanley M. Dunn

Introduction: The analysis and interpretation of electron micrographs of cells and tissues, often requires the accurate extraction of structural networks, which either provide immediate 2D or 3D information, or from which the desired information can be inferred. The images of these structures contain lines and/or curves whose orientation, lengths, and intersections characterize the overall network.Some examples exist of studies that have been done in the analysis of networks of natural structures. In, Sebok and Roemer determine the complexity of nerve structures in an EM formed slide. Here the number of nodes that exist in the image describes how dense nerve fibers are in a particular region of the skin. Hildith proposes a network structural analysis algorithm for the automatic classification of chromosome spreads (type, relative size and orientation).


Author(s):  
Jacob S. Hanker ◽  
Dale N. Holdren ◽  
Kenneth L. Cohen ◽  
Beverly L. Giammara

Keratitis and conjunctivitis (infections of the cornea or conjunctiva) are ocular infections caused by various bacteria, fungi, viruses or parasites; bacteria, however, are usually prominent. Systemic conditions such as alcoholism, diabetes, debilitating disease, AIDS and immunosuppressive therapy can lead to increased susceptibility but trauma and contact lens use are very important factors. Gram-negative bacteria are most frequently cultured in these situations and Pseudomonas aeruginosa is most usually isolated from culture-positive ulcers of patients using contact lenses. Smears for staining can be obtained with a special swab or spatula and Gram staining frequently guides choice of a therapeutic rinse prior to the report of the culture results upon which specific antibiotic therapy is based. In some cases staining of the direct smear may be diagnostic in situations where the culture will not grow. In these cases different types of stains occasionally assist in guiding therapy.


Author(s):  
S. Arumugam ◽  
Sarasa Bharati Arumugam

Adenoaas of the pituitary are no longer classified based on their tinctorial affinity to dyes. With the advent of the newer methods of sophisticated technology, it is now possible to classify. These depending upon the type of hormone secreted based either on histochemical techniques or on ultrastructural characteristics. The latter provides an insight into the cytoplasmic organelle morphology which offers a delightful feast to the eye as well.This paper presents the ultrastructural characters of the pituitary adenoma as seen in Madras. 171 adenomas (124 males and 47 females) were seen during 1972-1989, classified at the light microscope level as 159 chromophobe, 2 basophilic, 4 eosinophilic and 6 mixed adenomas.Ultrastructural examination showed that the sparsely granular prolactin cell adenoma is the commonest adenoma to be encountered closely followed by the growth hormone cell adenoma, null cell adenoma, the mixed cell adenoma and others.


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