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Journal articles on the topic 'Sequence similarity analysis'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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1

Wei, Dan, Qingshan Jiang, and Sheng Li. "A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases." International Journal of Nanotechnology and Molecular Computation 2, no. 4 (2010): 1–11. http://dx.doi.org/10.4018/978-1-60960-064-8.ch006.

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Similarity analysis of DNA sequences is a fundamental research area in Bioinformatics. The characteristic distribution of L-tuple, which is the tuple of length L, reflects the valuable information contained in a biological sequence and thus may be used in DNA sequence similarity analysis. However, similarity analysis based on characteristic distribution of L-tuple is not effective for the comparison of highly conservative sequences. In this paper, a new similarity measurement approach based on Triplets of Nucleic Acid Bases (TNAB) is introduced for DNA sequence similarity analysis. The new app

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2

Li, Hongliang, and Bin Liu. "BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo." PLOS Computational Biology 19, no. 6 (2023): e1011214. http://dx.doi.org/10.1371/journal.pcbi.1011214.

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As the key for biological sequence structure and function prediction, disease diagnosis and treatment, biological sequence similarity analysis has attracted more and more attentions. However, the exiting computational methods failed to accurately analyse the biological sequence similarities because of the various data types (DNA, RNA, protein, disease, etc) and their low sequence similarities (remote homology). Therefore, new concepts and techniques are desired to solve this challenging problem. Biological sequences (DNA, RNA and protein sequences) can be considered as the sentences of “the bo

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de Oliveira Martins, Leonardo, Alison E. Mather, and Andrew J. Page. "Scalable neighbour search and alignment with uvaia." PeerJ 12 (March 6, 2024): e16890. http://dx.doi.org/10.7717/peerj.16890.

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Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences. Uvaia overcomes this limitation by us

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Pacheco, Richard C., Jonas Moraes-Filho, Arlei Marcili, et al. "Rickettsia monteiroi sp. nov., Infecting the Tick Amblyomma incisum in Brazil." Applied and Environmental Microbiology 77, no. 15 (2011): 5207–11. http://dx.doi.org/10.1128/aem.05166-11.

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ABSTRACTFree-living adultAmblyomma incisumticks were collected in an Atlantic rainforest area at Intervales State Park, State of São Paulo, Brazil. From anA. incisumspecimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genesgltA,htrA,rrs, andsca1on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of thegltA,htrA,rrs, andsca1genes, respectively, were sequenced. By BLAST analysis, the partial se

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Van Reenen, C. A., W. H. Van Zyl, and L. M. T. Dicks. "Expression of the Immunity Protein of Plantaricin 423, Produced by Lactobacillus plantarum 423, and Analysis of the Plasmid Encoding the Bacteriocin." Applied and Environmental Microbiology 72, no. 12 (2006): 7644–51. http://dx.doi.org/10.1128/aem.01428-06.

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ABSTRACT Plantaricin 423 is a class IIa bacteriocin produced by Lactobacillus plantarum isolated from sorghum beer. It has been previously determined that plantaricin 423 is encoded by a plasmid designated pPLA4, which is now completely sequenced. The plantaricin 423 operon shares high sequence similarity with the operons of coagulin, pediocin PA-1, and pediocin AcH, with small differences in the DNA sequence encoding the mature bacteriocin peptide and the immunity protein. Apart from the bacteriocin operon, no significant sequence similarity could be detected between the DNA or translated seq

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Smallwood, M., J. N. Keen, and D. J. Bowles. "Purification and partial sequence analysis of plant annexins." Biochemical Journal 270, no. 1 (1990): 157–61. http://dx.doi.org/10.1042/bj2700157.

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A fractionation procedure for annexins involving Ca2(+)-dependent binding to exogenous phospholipid was applied to tomato suspension culture cells. Two polypeptides (34 kDa and 35.5 kDa) were purified and separated from each other and from contaminant pectic polysaccharide by ion-exchange chromatography. After proteolytic digestion of SDS/PAGE-purified products, N-terminal sequencing of the peptide fragments revealed substantial similarity to sequences of known members of the annexin family characterized from a range of animal tissues. In particular, sequence similarity to the 70-amino acid-re

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Xu, Fuyu, and Kate Beard. "A Unifying Framework for Analysis of Spatial-Temporal Event Sequence Similarity and Its Applications." ISPRS International Journal of Geo-Information 10, no. 9 (2021): 594. http://dx.doi.org/10.3390/ijgi10090594.

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Measures of similarity or differences between data objects are applied frequently in geography, biology, computer science, linguistics, logic, business analytics, and statistics, among other fields. This work focuses on event sequence similarity among event sequences extracted from time series observed at spatially deployed monitoring locations with the aim of enhancing the understanding of process similarity over time and geospatial locations. We present a framework for a novel matrix-based spatiotemporal event sequence representation that unifies punctual and interval-based representation of

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Shah, Mohammad Monir, Hirotoshi Iihara, Makiko Noda, et al. "dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus." International Journal of Systematic and Evolutionary Microbiology 57, no. 1 (2007): 25–30. http://dx.doi.org/10.1099/ijs.0.64205-0.

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In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean simila

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Györgyey, János, Danièle Vaubert, José I. Jiménez-Zurdo, et al. "Analysis of Medicago truncatula Nodule Expressed Sequence Tags." Molecular Plant-Microbe Interactions® 13, no. 1 (2000): 62–71. http://dx.doi.org/10.1094/mpmi.2000.13.1.62.

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Systematic sequencing of expressed sequence tags (ESTs) can give a global picture of the assembly of genes involved in the development and function of organs. Indeterminate nodules representing different stages of the developmental program are especially suited to the study of organogenesis. With the vector λHybriZAP, a cDNA library was constructed from emerging nodules of Medicago truncatula induced by Sinorhizobium meliloti. The 5′ ends of 389 cDNA clones were sequenced, then these ESTs were analyzed both by sequence homology search and by studying their expression in roots and nodules. Two

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Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (April 16, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.1.

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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2

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Abbas, Ali Hadi, Haider Abas AL saegh, and Furkan Sabbar ALaraji. "Sequence diversity and evolution of infectious bursal disease virus in Iraq." F1000Research 10 (September 2, 2021): 293. http://dx.doi.org/10.12688/f1000research.28421.2.

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Background: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare. Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2

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Lu, Yue, Long Zhao, Zhao Li, and Xiangjun Dong. "Genetic Similarity Analysis Based on Positive and Negative Sequence Patterns of DNA." Symmetry 12, no. 12 (2020): 2090. http://dx.doi.org/10.3390/sym12122090.

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Similarity analysis of DNA sequences can clarify the homology between sequences and predict the structure of, and relationship between, them. At the same time, the frequent patterns of biological sequences explain not only the genetic characteristics of the organism, but they also serve as relevant markers for certain events of biological sequences. However, most of the aforementioned biological sequence similarity analysis methods are targeted at the entire sequential pattern, which ignores the missing gene fragment that may induce potential disease. The similarity analysis of such sequences

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Nikhila, K. S., and Vrinda V. Nair. "Protein Sequence Similarity Analysis Using Computational Techniques." Materials Today: Proceedings 5, no. 1 (2018): 724–31. http://dx.doi.org/10.1016/j.matpr.2017.11.139.

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Hark Gan, Hin, Rebecca A. Perlow, Sharmili Roy, et al. "Analysis of Protein Sequence/Structure Similarity Relationships." Biophysical Journal 83, no. 5 (2002): 2781–91. http://dx.doi.org/10.1016/s0006-3495(02)75287-9.

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15

Ai, Liang, Jie Feng, and Yu Hua Yao. "A Novel Fast Approach for Protein Classification and Evolutionary Analysis." Match Communications in Mathematical and in Computer Chemistry 90, no. 2 (2023): 381–98. http://dx.doi.org/10.46793/match.90-2.381a.

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In this paper, we propose a new fast alignment-free method for protein sequence similarity and evolutionary analysis. First 20 natural amino acids are clustered into 6 groups based on their physicochemical properties, then a 12-dimensional vector is constructed based on the frequency and the average position of occurrence of amino acids in each reduced amino acid sequences. Finally, the Euclidean distance is used to measure the similarity and evolutionary distance between protein sequences. The test on three datasets shows that our method can cluster each protein sequence accurately, which ill

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Leonardo, F. C., A. F. da Cunha, M. J. da Silva, et al. "Analysis of the workers head transcriptome of the Asian subterranean termite, Coptotermes gestroi." Bulletin of Entomological Research 101, no. 4 (2010): 383–91. http://dx.doi.org/10.1017/s0007485310000556.

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AbstractThe lower termite, Coptotermes gestroi (Isoptera: Rhinotermitidae), is originally from Southeast Asia and has become a pest in Brazil. The main goal of this study was to survey C. gestroi transcriptome composition. To accomplish this, we sequenced and analyzed 3003 expressed sequence tags (ESTs) isolated from libraries of worker heads. After assembly, 695 uniESTs were obtained from which 349 have similarity with known sequences. Comparison with insect genomes demonstrated similarity, primarily with genes from Apis mellifera (28%), Tribolium castaneum (28%) and Aedes aegypti (10%). Nota

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Verma, Archana, Mr R.K.Bharti, and Prof R. K. Singh. "DNA sequence comparison based on Tabular Representation." INTERNATIONAL JOURNAL OF COMPUTERS & TECHNOLOGY 4, no. 1 (2013): 172–75. http://dx.doi.org/10.24297/ijct.v4i1c.3121.

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DNA sequence comparison remains as one of the critical steps in the analysis of phylogenetic relationships between species. In order to get quantitative comparison, we want to devise an algorithm that would use the tabular representation of DNA sequences. The tabular approach of representation captures the essence of the base composition and distribution of the sequence. In this contribution, we take the tabular notation for DNA sequences and then these tables are compared to find the similarity/dissimilarity measure of the sequences. We have developed algorithms for comparing DNA sequences. T

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Wirya, Gusti Ngurah Alit Susanta, I. Wayan Diksa Gargita, and I. Putu Sudiarta. "MOLECULAR IDENTIFICATION OF FUNGI THE CAUSAL AGENT OF STRAWBERRY WILT DISEASE IN BALI." International Journal of Biosciences and Biotechnology 7, no. 2 (2020): 64. http://dx.doi.org/10.24843/ijbb.2020.v07.i02.p02.

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The development of strawberry farming in Bali experiencing some obstacles that cause a decline in production, such as wilting disease. The disease was reported caused by the fungi base on morphological recognition. There are two fungi were recognized caused the strawberry wilt disease in Bali, they are from genus Verticillium and Fusarium. More specific information about causal agent of wilt disease in strawberry especially in Bali is needed. The one accurate identification is done through the molecular approach by analyzing DNA that encode the ribosomal DNA (rDNA). The 18S rDNA, including the

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GEREMIA, Roberto A., E. Alejandro PETRONI, Luis IELPI та Bernard HENRISSAT. "Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic α-mannosyltransferases". Biochemical Journal 318, № 1 (1996): 133–38. http://dx.doi.org/10.1042/bj3180133.

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A number of genes encoding bacterial glycosyltransferases have been sequenced during the last few years, but their low sequence similarity has prevented a straightforward grouping of these enzymes into families. The sequences of several bacterial α-mannosyltransferases have been compared using current alignment algorithms as well as hydrophobic cluster analysis (HCA). These sequences show a similarity which is significant but too low to be reliably aligned using automatic alignment methods. However, a region spanning approx. 270 residues in these proteins could be aligned by HCA, and several i

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Elzinga, Cees H., and Matthias Studer. "Normalization of Distance and Similarity in Sequence Analysis." Sociological Methods & Research 48, no. 4 (2019): 877–904. http://dx.doi.org/10.1177/0049124119867849.

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We explore the relations between the notion of distance and a feature set–based concept of similarity and show that this concept of similarity has a spatial interpretation that is complementary to distance: it is interpreted as “direction.” Furthermore, we show how proper normalization leads to distances that can be directly interpreted as dissimilarity: Closeness in normalized space implies and is implied by similarity of the same objects, while remoteness implies and is implied by dissimilarity. Finally, we show how, in research into destandardization of the life course, properly normalizing

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Drijver, Evert, Joep Stohr, Jaco Verweij, et al. "Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands." Microorganisms 8, no. 11 (2020): 1755. http://dx.doi.org/10.3390/microorganisms8111755.

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Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1–pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for the presence of both a blaCMY-2 gene and an IncI1–pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid

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Nasare, Kanchan, Amit Yadav, Anil K. Singh, K. B. Shivasharanappa, Y. S. Nerkar, and V. S. Reddy. "Molecular and Symptom Analysis Reveal the Presence of New Phytoplasmas Associated with Sugarcane Grassy Shoot Disease in India." Plant Disease 91, no. 11 (2007): 1413–18. http://dx.doi.org/10.1094/pdis-91-11-1413.

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A total of 240 sugarcane (Saccharum officinarum) plants showing phenotypic symptoms of sugarcane grassy shoot (SCGS) disease were collected from three states of India, Maharashtra, Karnataka, and Uttar Pradesh. Phytoplasmas were detected in all symptomatic samples by the polymerase chain reaction (PCR) amplification of phytoplasma-specific 16S rRNA gene and 16S-23S rRNA spacer region (SR) sequences. No amplification was observed when DNA from asymptomatic plant samples was used as a template. Sixteen samples were selected on the basis of phenotypic symptoms and geographic location, and cloning

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Chen, Junhong, Wei Dai, Hang Wang, Weiqiang Lei, Guangyuan Fang, and Dingzhen Dai. "Cloning and Expression of Pigeon-Derived Escherichia coli Type 1 Pilus Clusters and Analysis of Amino Acid Sequence Characteristics of Functional Proteins." Genes 15, no. 10 (2024): 1253. http://dx.doi.org/10.3390/genes15101253.

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Background: Type 1 pili, as an important virulence factor of E. coli, has certain homology between APEC and UPEC, but the homology degree is not clear enough. Objectives: This study aims to compare the homology between them. Methods: The recombinant bacteria were constructed by homologous recombination. The pili were observed by TEM, and the hemagglutination characteristics were determined by MHSA. The complete gene sequence was determined by sequencing, and the amino acid sequences of the functional proteins of type 1 pili of APEC and UPEC were compared. Results: TEM showed that they could ex

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G. S. Wijesiri, W. W. P. M. T. M. Karunasena,. "Application of Graph Theory in DNA similarity analysis of Evolutionary Closed Species." Psychology and Education Journal 58, no. 1 (2021): 3428–34. http://dx.doi.org/10.17762/pae.v58i1.1282.

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DNA is a complex molecule that consists of biological information that is passed down from generation to generation. With the evolution over time, there are different kinds of species that evolved from a common ancestor because of the occurrence of DNA sequence rearrangements. DNA sequence similarity analysis is a major challenge since the number of sequences is rapidly increasing in the DNA database. In this research, we based a mathematical method to analyze the similarity of two DNA sequences using Graph Theory. This mathematical method started by modeling a weighted directed graph for each

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Caputo, A., D. E. Sauer, and P. B. Rowe. "Nucleotide sequence and genomic organization of a human T lymphocyte serine protease gene." Journal of Immunology 145, no. 2 (1990): 737–44. http://dx.doi.org/10.4049/jimmunol.145.2.737.

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Abstract We have determined the nucleotide sequence of 4508 base pairs of human genomic DNA which contain the human serine esterase gene from cytotoxic T lymphocytes (SECT) (equivalent to the 1-3E cDNA clone) and include 879 bp of 5' flanking DNA and 393 bp of 3' flanking DNA. The gene consists of five exons of 88, 148, 136, 261, and 257 nucleotides separated by four introns of 1043, 455, 205, and 643 nucleotides. The location of introns with respect to protein coding sequences in the SECT gene is identical to that of the human cathepsin G and murine granzyme B genes. Comparison of SECT gene e

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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Soo-Yong Kim, and Md Oliur Rahman. "Molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus inferred from analysis of internal transcribed spacer sequences." Bangladesh Journal of Plant Taxonomy 22, no. 2 (2015): 111–18. http://dx.doi.org/10.3329/bjpt.v22i2.26072.

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The present study explored molecular phylogenetic analysis of 28 species of Euphorbia L. for the identification and establishment of molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus based on the internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA). The sequence similarity search using Basic Local Alignment Search Tool (BLAST) of the ITS sequence of E. scordifolia showed the closest sequence similarity to E. supina Raf. The analysis of ITS sequence data revealed four major clades consistent with subgeneric classificat

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Bielińska-Wąż, Dorota, Piotr Wąż, Agata Błaczkowska, et al. "Mathematical Modeling in Bioinformatics: Application of an Alignment-Free Method Combined with Principal Component Analysis." Symmetry 16, no. 8 (2024): 967. http://dx.doi.org/10.3390/sym16080967.

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In this paper, an alignment-free bioinformatics technique, termed the 20D-Dynamic Representation of Protein Sequences, is utilized to investigate the similarity/dissimilarity between Baculovirus and Echinococcus multilocularis genome sequences. In this method, amino acid sequences are depicted as 20D-dynamic graphs, comprising sets of “material points” in a 20-dimensional space. The spatial distribution of these material points is indicative of the sequence characteristics and is quantitatively described by sequence descriptors akin to those employed in dynamics, such as coordinates of the cen

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Powell, J. F., Y. P. Hsu, W. Weyler, et al. "The primary structure of bovine monoamine oxidase type A. Comparison with peptide sequences of bovine monoamine oxidase type B and other flavoenzymes." Biochemical Journal 259, no. 2 (1989): 407–13. http://dx.doi.org/10.1042/bj2590407.

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We have isolated cDNA clones believed to encompass the full-length coding sequences for a subunit of bovine monoamine oxidase type A (MAO-A). The clones code for an apoprotein of 527 amino acid residues corresponding to a molecular mass of 59,806 Da. The inferred protein sequences show an overall similarity of 68% with partial amino acid sequences of bovine type B MAO (about 41% of the total sequence), as well as a greater similarity (greater than 90%) with some regions including that for the published sequence of the flavin-binding region. Sequence comparisons indicate that these two forms of

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Kholiq, Hibban, Mamika Ujianita Romdhini, and Marliadi Susanto. "Algoritma Needleman-Wunsch dalam Menentukan Tingkat Kemiripan Urutan DNA Rusa Timor (Cervus timorensis) dan Rusa Merah (Cervus elaphus)." EIGEN MATHEMATICS JOURNAL 3, no. 2 (2020): 125. http://dx.doi.org/10.29303/emj.v3i2.65.

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Sequence alignment is a basic method in sequence analysis. This method is used to determine the similaritiy level of DNA sequences. The Needleman-Wunsch algorithm is an algorithm that can be used to solve the problem of sequence alignment. This research shows that the relation T (i, j) used in the Needleman-Wunsch algorithm is a function where T: (ℕ0 ℕ0) → ℤ. The function T (i, j) is a recursive function. Moreover, DNA sequence data used are DNA sequences from the Timor Deer, which are the identities of the provinces of West Nusa Tenggara and Red Deer, which are typical deer from the European

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Killer, J., J. Kopečný, J. Mrázek, et al. "Bifidobacterium actinocoloniiforme sp. nov. and Bifidobacterium bohemicum sp. nov., from the bumblebee digestive tract." International Journal of Systematic and Evolutionary Microbiology 61, no. 6 (2011): 1315–21. http://dx.doi.org/10.1099/ijs.0.022525-0.

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Our previous study, based primarily on PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequencing, focused on the isolation of four bifidobacterial groups from the digestive tract of three bumblebee species. In that study, we proposed that these isolated groups potentially represented novel species of the family Bifidobacteriaceae. One of the four, Bifidobacterium bombi, has been described recently. Strains representing two of the other groups have been classified as members of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase act

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Bux, Bhagwan, Pankaj Kumar, Mahesh Kumar Bharti, and Jitender Singh. "Molecular Characterization of Proline Rich Regions in Lens culinaris under Abiotic Stress." International Journal of Bio-resource and Stress Management 13, no. 6 (2022): 638–45. http://dx.doi.org/10.23910/1.2022.2935a.

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The present study attempt was made to isolate and characterized Lens culinaris full length proline rich gene. EST Sequences of proline gene (GT-622346.1) from Lens culinaris was retrieved from Genbank. This sequence was used as query against chickpea. Similarity sequence search has shown up to 90% similarity with EST sequence of chickpea having the Accession No. GR 398344 and up to 85% similarity with EST sequence having Accession No. GT 622346 of Lens culinaris. The positive results were subjected to sequencing and were further in-silico analysis carried out. BLASTp of the lentil sequence sho

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Wilson, Clarke. "The Structure of Stages in the Evaluation Cycle: An Event Sequence Analysis." Canadian Journal of Program Evaluation 15, no. 1 (2000): 41–55. http://dx.doi.org/10.3138/cjpe.015.003.

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Abstract: From time to time, research on evaluation issues deals with a sequence of events or episodes which an analyst would prefer to examine in its entirety rather than event by event. However, quantitative methods for comparing sequences of events or activities and analyzing their similarity among populations and samples have rarely been applied in social research. This article describes the tasks undertaken during the cycle of evaluation of housing programs by CMHC prior to 1997 and analyses the major evaluation products in terms of the similarity of constituent tasks. A brief introductio

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Yang, Tae-Jin, Jung-Sun Kim, Ki-Byung Lim, et al. "The KoreaBrassicaGenome Project: a Glimpse of theBrassicaGenome Based on Comparative Genome Analysis WithArabidopsis." Comparative and Functional Genomics 6, no. 3 (2005): 138–46. http://dx.doi.org/10.1002/cfg.465.

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A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) ofBrassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones fromBrassicachromosome 1 revealed their homeologo

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Pereira, Maria das Graças C., Edward R. Atwill, Melissa R. Crawford, and Rance B. Lefebvre. "DNA Sequence Similarity between California Isolates of Cryptosporidium parvum." Applied and Environmental Microbiology 64, no. 4 (1998): 1584–86. http://dx.doi.org/10.1128/aem.64.4.1584-1586.1998.

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ABSTRACT We evaluated whether nucleic acid amplification with primers specific for Cryptosporidium parvum followed by automated DNA sequence analysis of the PCR amplicons could differentiate between California isolates of C. parvum obtained from livestock, humans, and feral pigs. Almost complete sequence identity existed among the livestock isolates and between the livestock and human isolates. DNA sequences from feral pig isolates differed from those from livestock and humans by 1.0 to 1.2%. The reference sequence obtained by Laxer et al. (M. A. Laxer, B. K. Timblin, and R. J. Patel, Am. J. T

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Thompson, F. L., D. Gevers, C. C. Thompson, et al. "Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis." Applied and Environmental Microbiology 71, no. 9 (2005): 5107–15. http://dx.doi.org/10.1128/aem.71.9.5107-5115.2005.

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ABSTRACT We analyzed the usefulness of rpoA, recA, and pyrH gene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documented Vibrionaceae strains and 16 presumptive Vibrio isolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-

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Su, Jie, and Junpeng Bao. "A Wavelet Transform Based Protein Sequence Similarity Model." Applied Mathematics & Information Sciences 7, no. 3 (2013): 1103–10. http://dx.doi.org/10.12785/amis/070330.

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Beccari, T., J. Hoade, A. Orlacchio та J. L. Stirling. "Cloning and sequence analysis of a cDNA encoding the α-subunit of mouse β-N-acetylhexosaminidase and comparison with the human enzyme". Biochemical Journal 285, № 2 (1992): 593–96. http://dx.doi.org/10.1042/bj2850593.

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cDNAs encoding the mouse beta-N-acetylhexosaminidase alpha-subunit were isolated from a mouse testis library. The longest of these (1.7 kb) was sequenced and showed 83% similarity with the human alpha-subunit cDNA sequence. The 5′ end of the coding sequence was obtained from a genomic DNA clone. Alignment of the human and mouse sequences showed that all three putative N-glycosylation sites are conserved, but that the mouse alpha-subunit has an additional site towards the C-terminus. All eight cysteines in the human sequence are conserved in the mouse. There are an additional two cysteines in t

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Gancheva, Veska, and Hristo Stoev. "Optimization and Performance Analysis of CAT Method for DNA Sequence Similarity Searching and Alignment." Genes 15, no. 3 (2024): 341. http://dx.doi.org/10.3390/genes15030341.

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Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of biological data. Sequence comparisons are the best way to investigate and understand the biological functions and evolutionary relationships between genes on the basis of the alignment of two or more DNA sequences in order to maximize the identity level and degree of similarity. This

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Xu, Pan, An Chun Cheng, Ming Shu Wang, De Kang Zhu, and Xiao Jia Wang. "Sequence Analysis of the Riemerella anatipestifer OmpAMotB Gene(ORF 648bp) by Bioinformatics." Advanced Materials Research 647 (January 2013): 381–85. http://dx.doi.org/10.4028/www.scientific.net/amr.647.381.

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The OmpA/MotB gene from RA by our lab was sequenced. And the molecular characteristic of this gene was analyzed with bioinformatics software. The result indicated that an open reading frame(ORF) containing 648bp nucleotides was preliminarily identified by aligning with gene bank database by software of BlastN and ORF Finder. The GC content of RA OmpA/MotB gene was 36.88% and encoded a 215 amino acids in this peptide. And from the analysis results we know that this gene sequence didn’t contain a successive at least two rare codons string. Phylogenetic tree of the amino acids sequences showed th

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Barik, Sasmita, Chandra Mohan Sidappa, Mohini Saini, et al. "Sequence-Based Appraisal of the Genes Encoding Neck and Carbohydrate Recognition Domain of Conglutinin in Blackbuck (Antilope cervicapra) and Goat (Capra hircus)." BioMed Research International 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/389150.

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Conglutinin, a collagenous C-type lectin, acts as soluble pattern recognition receptor (PRR) in recognition of pathogens. In the present study, genes encoding neck and carbohydrate recognition domain (NCRD) of conglutinin in goat and blackbuck were amplified, cloned, and sequenced. The obtained 488 bp ORFs encoding NCRD were submitted to NCBI with accession numbers KC505182 and KC505183. Both nucleotide and predicted amino acid sequences were analysed with sequences of other ruminants retrieved from NCBI GenBank using DNAstar and Megalign5.2 software. Sequence analysis revealed maximum similar

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Mohanta, Tapan Kumar. "Corona virus (CoVid19) genome: genomic and biochemical analysis revealed its possible synthetic origin." Journal of Applied Biotechnology & Bioengineering 7, no. 5 (2020): 200–213. http://dx.doi.org/10.15406/jabb.2020.07.00235.

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The Severe acute respiratory syndrome (SARS) corona virus 2 SARS-CoV-2 mediated epidemic is a global pandemic. It has evolved as a curse to the human civilization and at the present situation, where most of the cities in the world are on lockdown. The first genome sequence data of SARS-CoV-2 (CoVid19) and their reports that followed concluded that it was a member of the genus Betacoronavirus and has a bat reservoir. To understand its origin and evolution, we conducted a deep comparative study by comparing the genomes of bat SARS CoV and other SARS CoVs (including human SARS CoV of German isola

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Shams, Mahmoud Y., Romany M. Farag, Dalia A. Aldawody, et al. "Unveiling Similarities in the Code of Life: A Detailed Exploration of DNA Sequence Matching Algorithm." Neutrosophic Systems with Applications 22 (October 1, 2024): 13–30. http://dx.doi.org/10.61356/j.nswa.2024.22369.

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Identifying similar DNA sequences is crucial in various biological research endeavors. This paper delves into the intricate workings of a specific algorithm designed for this purpose. We provide a systematic explanation, exploring how the algorithm handles user input, reads stored DNA sequences, utilizes the Word2Vec model for vector representation, and calculates sequence similarity using diverse metrics like Cosine Similarity and Neutrosophic Distance. Additionally, the paper explores the incorporation of neutrosophic values to account for uncertainty in the comparisons. Finally, we discuss

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Michalek, Wolfgang, Gottfried Künzel, and Andreas Graner. "Sequence analysis and gene identification in a set of mapped RFLP markers in barley (Hordeum vulgare)." Genome 42, no. 5 (1999): 849–53. http://dx.doi.org/10.1139/g99-036.

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The "Igri/Franka" (I/F) map ranks among the most comprehensive genetic linkage maps of barley (Hordeum vulgare), containing a large number of markers derived from cDNA and genomic PstI clones. Fourty-three cDNA clones and 259 genomic clones were at least partially sequenced and compared with the major data bases of protein and nucleic acid sequences. Of the cDNA clones, 53% show significant similarity to known sequences in protein data bases. A comparison of sequences from genomic clones to nucleic acid sequence data bases revealed similarities for 9% of the clones. For cDNA sequences analyzed

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D'Hoostelaere, L. A., and D. Klinman. "Characterization of new mouse V kappa groups." Journal of Immunology 145, no. 8 (1990): 2706–12. http://dx.doi.org/10.4049/jimmunol.145.8.2706.

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Abstract A lambda gt10 BXSB spleen cDNA library was screened with a DNA probe for the C kappa region. Forty individual C kappa+ phages were tested for hybridization with DNA probes representing 11 V kappa region groups. Of the phage inserts large enough to contain V kappa region sequences, 3 were negative for hybridization with all 11 V kappa region probes. The inserts from those three were subcloned, sequenced, and compared with V kappa region sequences in the gene bank. One was identical to 87.92.6 for the region sequenced (a member of V kappa RF). The second showed 93.8% sequence similarity

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POPESCU, D., IONELA MIRELA NEAGOE, SUZANA E. CILIEVICI, DIANA R. CONSTANTIN, and V. I. R. NICULESCU. "ANALYSIS OF THE CRYPTOSPORIDIUM SPP GP60 GENE VARIABILITY APPLYING INFORMATION THEORY." Romanian Journal of Biophysics 34, no. 1 (2024): 1–12. http://dx.doi.org/10.59277/rjb.2024.1.01.

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In this paper we used statistical methods to understand the genetic information of DNA considered as a statistical system. The alphabet of a DNA sequence is defined by the four nucleotides: adenine, cytosine, guanine, and thymine. The order of nucleotides along the DNA sequences encodes the genetic information. We have analyzed three Cryptosporidium DNA sequences: one DNA sequence isolated and analyzed in our laboratory and two DNA reference sequences from the public database GenBank. Each DNA sequence is considered as a statistical system and is represented by a random variable and an associa

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Abd Elwahaab, Marwa A., Mervat M. Abo-Elkhier, and Moheb I. Abo el Maaty. "A Statistical Similarity/Dissimilarity Analysis of Protein Sequences Based on a Novel Group Representative Vector." BioMed Research International 2019 (May 8, 2019): 1–9. http://dx.doi.org/10.1155/2019/8702968.

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Similarity/dissimilarity analysis is a key way of understanding the biology of an organism by knowing the origin of the new genes/sequences. Sequence data are grouped in terms of biological relationships. The number of sequences related to any group is susceptible to be increased every day. All the present alignment-free methods approve the utility of their approaches by producing a similarity/dissimilarity matrix. Although this matrix is clear, it measures the degree of similarity among sequences individually. In our work, a representative of each of three groups of protein sequences is intro

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Bellachioma, G., J. L. Stirling, A. Orlacchio, and T. Beccari. "Cloning and sequence analysis of a cDNA clone coding for the mouse GM2 activator protein." Biochemical Journal 294, no. 1 (1993): 227–30. http://dx.doi.org/10.1042/bj2940227.

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A cDNA (1.1 kb) containing the complete coding sequence for the mouse GM2 activator protein was isolated from a mouse macrophage library using a cDNA for the human protein as a probe. There was a single ATG located 12 bp from the 5‘ end of the cDNA clone followed by an open reading frame of 579 bp. Northern blot analysis of mouse macrophage RNA showed that there was a single band with a mobility corresponding to a size of 2.3 kb. We deduce from this that the mouse mRNA, in common with the mRNA for the human GM2 activator protein, has a long 3′ untranslated sequence of approx. 1.7 kb. Alignment

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Killer, J., I. Sedláček, V. Rada, J. Havlík, and J. Kopečný. "Reclassification of Bifidobacterium stercoris Kim et al. 2010 as a later heterotypic synonym of Bifidobacterium adolescentis." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (2013): 4350–53. http://dx.doi.org/10.1099/ijs.0.054957-0.

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The taxonomic position of Bifidobacterium stercoris Eg1T ( = JCM 15918T) based on comparative 16S rRNA gene and hsp60 sequence analyses was found to be controversial, as the strain showed high similarity to the type strain of Bifidobacterium adolescentis , CCUG 18363T. Therefore, the relationship between the two species was investigated by a taxonomic study that included, in addition to re-evaluation of the 16S rRNA gene sequence, determination of DNA–DNA binding and multilocus sequence analysis (MLSA) of housekeeping genes encoding the DNA-directed RNA polymerase B subunit (rpoC), putative xy

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Asare, James Owusu, Justice Kwame Appati, and Kwaku Darkwah. "Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment." International Journal of Mathematics and Mathematical Sciences 2020 (June 1, 2020): 1–9. http://dx.doi.org/10.1155/2020/3858057.

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Global sequence alignment is one of the most basic pairwise sequence alignment procedures used in molecular biology to understand the similarity that arises among the structure, function, or evolutionary relationship between two nucleotide sequences. The general algorithm associated with global sequence alignment is the dynamic programming algorithm of Needleman and Wunsch. In this paper, patterns are exploited in the score matrix of the Needleman–Wunsch algorithm. With the help of some examples, the general patterns realized are formulated as new a priori propositions and corollaries that are

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Begum, RA, MT Alam, H. Jahan, and MS Alam. "Partial sequence analysis of mitochondrial cytochrome B gene of Labeo calbasu of Bangladesh." Journal of Biodiversity Conservation and Bioresource Management 5, no. 1 (2019): 25–30. http://dx.doi.org/10.3329/jbcbm.v5i1.42182.

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Labeo calbasu (Family Cyprinidae) was studied at DNA level to know genetic diversity within and between species. The mitochondrial cytochrome b (cyt-b) gene of L. calbasu was sequenced and compared to the corresponding sequences of other Labeo species. DNA was isolated from the tissue sample of L. calbasu using phenol: chloroform extraction method. Forward and reverse primers were designed to amplify the target region of cytochrome b gene. A standard PCR protocol was used for the amplification of the desired region. Then, the forward and reverse sequences obtained were aligned and edited to fi

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