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Journal articles on the topic 'Basic Local Alignment Search Tool'

Author: Grafiati

Published: 4 June 2021

Last updated: 4 February 2022

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1

Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman. "Basic local alignment search tool." Journal of Molecular Biology 215, no. 3 (October 1990): 403–10. http://dx.doi.org/10.1016/s0022-2836(05)80360-2.

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2

Mount, David W. "Using the Basic Local Alignment Search Tool (BLAST)." Cold Spring Harbor Protocols 2007, no. 7 (July 2007): pdb.top17. http://dx.doi.org/10.1101/pdb.top17.

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Wang, Hui, Leixiao Li, Chengdong Zhou, Hao Lin, and Dan Deng. "Spark-based Parallelization of Basic Local Alignment Search Tool." International Journal Bioautomation 24, no. 1 (March 2020): 87–98. http://dx.doi.org/10.7546/ijba.2020.24.1.000767.

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Eric, S. Donkor, T. K. D. Dayie Nicholas, and K. Adiku Theophilus. "Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)." Journal of Bioinformatics and Sequence Analysis 6, no. 1 (April 30, 2014): 1–6. http://dx.doi.org/10.5897/ijbc2013.0086.

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Konerding, D. "An Essential Guide to the Basic Local Alignment Search Tool: BLAST." Briefings in Bioinformatics 5, no. 1 (January 1, 2004): 93–94. http://dx.doi.org/10.1093/bib/5.1.93.

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O’Driscoll, Aisling, Vladislav Belogrudov, John Carroll, Kai Kropp, Paul Walsh, Peter Ghazal, and Roy D. Sleator. "HBLAST: Parallelised sequence similarity – A Hadoop MapReducable basic local alignment search tool." Journal of Biomedical Informatics 54 (April 2015): 58–64. http://dx.doi.org/10.1016/j.jbi.2015.01.008.

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Chen, Ying, Weicai Ye, Yongdong Zhang, and Yuesheng Xu. "High speed BLASTN: an accelerated MegaBLAST search tool." Nucleic Acids Research 43, no. 16 (2015): 7762–68. http://dx.doi.org/10.1093/nar/gkv784.

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Abstract Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretc

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Nowicki, Marek, Davit Bzhalava, and Piotr BaŁa. "Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in Java Library." Journal of Computational Biology 25, no. 8 (August 2018): 871–81. http://dx.doi.org/10.1089/cmb.2018.0079.

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Matsuda, Fumio, Hiroshi Tsugawa, and Eiichiro Fukusaki. "Method for Assessing the Statistical Significance of Mass Spectral Similarities Using Basic Local Alignment Search Tool Statistics." Analytical Chemistry 85, no. 17 (August 14, 2013): 8291–97. http://dx.doi.org/10.1021/ac401564v.

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Guo, Xinyu, Hong Wang, and Vijay Devabhaktuni. "A Systolic Array-Based FPGA Parallel Architecture for the BLAST Algorithm." ISRN Bioinformatics 2012 (September 4, 2012): 1–11. http://dx.doi.org/10.5402/2012/195658.

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A design of systolic array-based Field Programmable Gate Array (FPGA) parallel architecture for Basic Local Alignment Search Tool (BLAST) Algorithm is proposed. BLAST is a heuristic biological sequence alignment algorithm which has been used by bioinformatics experts. In contrast to other designs that detect at most one hit in one-clock-cycle, our design applies a Multiple Hits Detection Module which is a pipelining systolic array to search multiple hits in a single-clock-cycle. Further, we designed a Hits Combination Block which combines overlapping hits from systolic array into one hit. Thes

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Uthayakumar, Muthukumarasamy, Govindhan Sowmiya, Radhakrishnan Sabarinathan, N. Udayaprakash, M. Kirti Vaishnavi, and Kanagaraj Sekar. "BSSB:BLASTServer for Structural Biologists." Journal of Applied Crystallography 44, no. 3 (April 2, 2011): 651–54. http://dx.doi.org/10.1107/s0021889811008387.

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The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processingBLASToutput, but none of them provide three-dimensional structure visualization. This shortcoming has been addressed in the proposed toolBLASTServer for Structural Biologists (BSSB), which maps aBLASToutput onto the three-dimensional structure of the subject protein. The three-dimensional structure of the subject pro

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Santelli, Roberto V., and Fábio Siviero. "A search for homologues of plant photoreceptor genes and their signaling partners in the sugarcane expressed sequence tag (Sucest) database." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 49–53. http://dx.doi.org/10.1590/s1415-47572001000100008.

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A search in the sugarcane expressed sequence tag (SUCEST) database for homologues of plant genes involved in photo-sensory mechanisms was carried out using the basic local alignment tool (BLAST). Our results shown that known elements (phytochromes, cryptochromes and phototoprin) present in Arabidopsis and other higher plants were detected with low e-values. We also searched for proteins interacting with photoreceptors in primary or downstream signaling events. One putative homologue for a protein postulated to be a primary element in phytochrome signaling pathways was identified, as were other

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Brodmann, P. D., G. Nicholas, P. Schaltenbrand, and E. C. Ilg. "Identifying unknown game species: experience with nucleotide sequencing of the mitochondrial cytochrome b gene and a subsequent basic local alignment search tool search." European Food Research and Technology 212, no. 4 (March 7, 2001): 491–96. http://dx.doi.org/10.1007/s002170000284.

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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 (December 30, 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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West, Ruth, Jeff Burke, Cheryl Kerfeld, Eitan Mendelowitz, Thomas Holton, J. P. Lewis, Ethan Drucker, and Weihong Yan. "Both and Neither: in silico v1.0, Ecce Homology." Leonardo 38, no. 4 (August 2005): 286–93. http://dx.doi.org/10.1162/0024094054762089.

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Ecce Homology, a physically interactive new-media work, visualizes genetic data as calligraphic forms. A novel computer-vision user interface allows multiple participants, through their movement in the installation space, to select genes from the human genome for visualizing the Basic Local Alignment Search Tool (BLAST), a primary algorithm in comparative genomics. Ecce Homology was successfully installed in the UCLA Fowler Museum, 6 November 2003–4 January 2004.

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Oany, Arafat Rahman, Tahmina Pervin Jyoti, and Shah Adil Ishtiyaq Ahmad. "An in Silico Approach for Characterization of an Aminoglycoside Antibiotic-Resistant Methyltransferase Protein from Pyrococcus furiosus (DSM 3638)." Bioinformatics and Biology Insights 8 (January 2014): BBI.S14620. http://dx.doi.org/10.4137/bbi.s14620.

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Pyrococcus furiosus is a hyperthermophilic archaea. A hypothetical protein of this archaea, PF0847, was selected for computational analysis. Basic local alignment search tool and multiple sequence alignment (MSA) tool were employed to search for related proteins. Both the secondary and tertiary structure prediction were obtained for further analysis. Three-dimensional model was assessed by PROCHECK and QMEAN6 programs. To get insights about the physical and functional associations of the protein, STRING network analysis was performed. Binding of the SAM (S-adenosyl-1-methionine) ligand with ou

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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Gábor Gyulai, and Arun K. Pandey. "Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan." Bangladesh Journal of Plant Taxonomy 21, no. 1 (June 23, 2014): 33–42. http://dx.doi.org/10.3329/bjpt.v21i1.19256.

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The present study explored the use of internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA) for identification of Echinops mandavillei Kit Tan, an endemic species to Saudi Arabia. The sequence similarity search using Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses of the ITS sequence of E. mandavillei Kit Tan showed high level of sequence similarity (98%) with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. mandavillei could have a potential use for molecular genotyping.DOI

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Ali, M. Ajmal, Fahad M. Al-Hemaid, Ritesh K. Choudhary, Joongku Lee, Soo-Yong Kim, and M. A. Rub. "Status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae) inferred from combined nuclear ribosomal and chloroplast sequence data." Bangladesh Journal of Plant Taxonomy 20, no. 2 (December 22, 2013): 233–38. http://dx.doi.org/10.3329/bjpt.v20i2.17397.

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The present study focuses on the status of Reseda pentagyna Abdallah & A.G. Miller (Resedaceae). The internal transcribed spacer (ITS) region of nuclear ribosomal DNA and chloroplast trnL-F gene of the questioned species were sequenced. The Basic Local Alignment Search Tool (BLAST) search showed maximum identity with R. stenostachya. The parsimony analysis of ITS, trnL-F and combined sequences data analyses revealed grouping of Reseda species consistent with established taxonomic sections of the genus, R. pentagyna showed proximity with R. stenostachya (100% bootstrap support), nested with

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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 (December 28, 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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20

Hentabli, Hamza, Faisal Saeed, Ammar Abdo, and Naomie Salim. "A New Graph-Based Molecular Descriptor Using the Canonical Representation of the Molecule." Scientific World Journal 2014 (2014): 1–10. http://dx.doi.org/10.1155/2014/286974.

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Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual s

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21

Seong, Eun Soo, Ji Hye Yoo, Jae Hoo Choi, Chang Heum Kim, Mi Ran Jeon, Byeong Ju Kang, Jae Geun Lee, Seon Kang Choi, Bimal Kumar Ghimire, and Chang Yeon Yu. "Expressed Sequence Tags Analysis and Design of Simple Sequence Repeats Markers from a Full-Length cDNA Library inPerilla frutescens(L.)." International Journal of Genomics 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/679548.

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Perilla frutescensis valuable as a medicinal plant as well as a natural medicine and functional food. However, comparative genomics analyses ofP. frutescensare limited due to a lack of gene annotations and characterization. A full-length cDNA library fromP. frutescensleaves was constructed to identify functional gene clusters and probable EST-SSR markers via analysis of 1,056 expressed sequence tags. Unigene assembly was performed using basic local alignment search tool (BLAST) homology searches and annotated Gene Ontology (GO). A total of 18 simple sequence repeats (SSRs) were designed as pri

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22

Terai, Masanori, and Robert D. Burk. "Characterization of a novel genital human papillomavirus by overlapping PCR: candHPV86 identified in cervicovaginal cells of a woman with cervical neoplasia." Journal of General Virology 82, no. 9 (September 1, 2001): 2035–40. http://dx.doi.org/10.1099/0022-1317-82-9-2035.

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A novel human papillomavirus (HPV), candHPV86, was cloned and characterized from cervicovaginal cells obtained from a 37-year-old Hispanic woman with cervical intraepithelial neoplasia grade 1 (CIN1) using an overlapping PCR technique. Primers were designed by phylogenetic alignment of closely related HPV genomes using the L1 fragment sequence amplified by GP5+/6+. The 7983 bp complete nucleotide sequence of the HPV genome was determined by sequence walking. A basic local alignment sequence tool (BLAST) homology search using the L1 open reading frame demonstrated that this HPV was most closely

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De Oliveira Andrade, Luis Jesuino, Gustavo Magno Baptista, Juliane Santos Dias, Alcina Maria Vinhaes Bittencourt, and Larissa Santos França. "Relationship between vitiligo and Hashimoto's thyroiditis." Revista de Ciências Médicas e Biológicas 16, no. 1 (July 14, 2017): 5. http://dx.doi.org/10.9771/cmbio.v16i1.17619.

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<p><strong>Background</strong>: Vitiligo is a multifactorial acquired depigmenting disorder, characterized by a spontaneous loss of functional melanocytes from the epidermis. Vitiligo and Hashimoto's thyroiditis (HT) often occur in association and seem to be characterized by an autoimmune process. The vitiligo associated with HT suggests genetic homologies between them.</p><p><strong>Objective</strong>: To identify protein sequence homology between melanocyte protein (Pmel) and thyroid peroxidase (TPO), using bioinformatics tools, to propose an initial

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Shabaan, Amr M., Magdy M. Mohamed, Mohga S. Abdallah, Hayat M. Ibrahim, and Amr M. Karim. "Analysis of Schistosoma mansoni genes using the expressed sequence tag approach." Acta Biochimica Polonica 50, no. 1 (March 31, 2003): 259–68. http://dx.doi.org/10.18388/abp.2003_3735.

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Expressed sequence tags (ESTs) are partial cDNA sequences read from both ends of random expressed gene fragments used for discovering new genes. DNA libraries from four different developmental stages of Schistosoma mansoni used in this study generated 141 ESTs representing about 2.5% of S. mansoni sequences in dbEST. Sequencing was done by the dideoxy chain termination method. The sequences were submitted to GenBank for homology searching in nonredundant databases using Basic Local Alignment Search Tool for DNA (BLASTN) alignment and for protein (BLASTX) alignment at the National Center for Bi

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Taariwuan, Marlin Bernadet, Jantje Ngangi, Yermia Mokosuli, and Sukmarayu Gedoan. "DNA Barcoding Dalugha (Cyrtosperma Merkusii) di Kepulauan Talaud dan Minahasa Selatan Berdasarkan Gen rbcL." JURNAL BIOS LOGOS 11, no. 2 (September 4, 2021): 134. http://dx.doi.org/10.35799/jbl.v11i2.34452.

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(Article History: Received June 28, 2021; Revised August 30, 2021; Accepted Sept 3, 2021) ABSTRAKDalugha (Cyrtospera merkusii (Hassk.)Schott) merupakan tanaman endemik Sulawesi Utara yang digunakan sebagai pangan alternatif (penganti beras). Penelitian ini bertujuan untuk membandingkan spesies daluga di Kepulauan Talaud dan Minahasa Selatan menggunakan DNA barcode gen rbcL (ribulose 1,5 bisphosphate carboxylase large). Perbandingan barcode DNA yang dilakukan pada empat sampel yang berbeda lokasi tersebut keduanya menghasilkan tingkat kesamaan 100% (identik). Dengan demikian, tidak ada variasi

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Chen, Xin, Li Xu, Xiao-juan Zong, Hai-rong Wei, Jia-wei Wang, Dong-zi Zhu, Yue Tan, Mao-run Fu, and Qing-zhong Liu. "Transcriptome Analysis, Marker Discovery and Pigment Biosynthesis of Red-leaf Juglans regia." Journal of Applied Biotechnology 5, no. 2 (June 4, 2017): 20. http://dx.doi.org/10.5296/jab.v5i2.11345.

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Red-leaf trait rarely occurs in Juglans regia, and the genetic mechanism underlying this phenomenon is still unknown. In this study, we attempted to provide insight into the comprehensive transcriptome of red-leaf J. regia by RNA-Seq using Illumina SeqTM2000 platform. A total of 33,488,602 high-quality reads (3.35G cleans bases) were obtained and assembled into 53,782 unigenes. A total of 3,683 unigenes were annotated by using basic local alignment search tool to search against protein databases, All the matched unigenes were categorized by gene ontology analysis, and 3,466 were assigned to me

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Dias, R., M. G. Xavier, F. D. Rossi, M. V. Neves, T. A. P. Lange, A. Giongo, C. A. F. De Rose, and E. W. Triplett. "MPI-blastn and NCBI-TaxCollector: Improving metagenomic analysis with high performance classification and wide taxonomic attachment." Journal of Bioinformatics and Computational Biology 12, no. 03 (June 2014): 1450013. http://dx.doi.org/10.1142/s0219720014500139.

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Metagenomic sequencing technologies are advancing rapidly and the size of output data from high-throughput genetic sequencing has increased substantially over the years. This brings us to a scenario where advanced computational optimizations are requested to perform a metagenomic analysis. In this paper, we describe a new parallel implementation of nucleotide BLAST (MPI-blastn) and a new tool for taxonomic attachment of Basic Local Alignment Search Tool (BLAST) results that supports the NCBI taxonomy (NCBI-TaxCollector). MPI-blastn obtained a high performance when compared to the mpiBLAST and

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Saleky, Dandi, and Sendy Lely Merly. "Molecular Phylogenetic of Cerithidea anticipata (Iredale, 1929) (Mollusk: Gastropod)." Jurnal Ilmiah PLATAX 9, no. 1 (February 10, 2021): 9. http://dx.doi.org/10.35800/jip.9.1.2021.32422.

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Species identification is very important and an important part of bioecological studies, so phylogenetic studies of Cerithidea anticipata (Iredale, 1929) was conducted in September 2020 to identify C. anticipata (Iredale, 1929) based on DNA barcoding techniques. Samples of C. anticipata (Iredale, 1929) were collected from the mangrove ecosystem of Payum Merauke Beach Papua (Indonesia), where the genes used were primary COI Gene forward LCO1490 and reverse HCO2198. The result of DNA amplification obtained DNA sequence length of 660 bp, then based on the identification of Basic Local Alignment S

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Stevic, Nevena, Eleonora Capelja, Vladislava Galovic, Milana Novakovic, and Maja Karaman. "Molecular characterization of some lignicolous species from fungal culture collection." Genetika 46, no. 1 (2014): 235–42. http://dx.doi.org/10.2298/gensr1401235s.

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Culture collections of microorganisms, including fungi, are strain deposits recognised as Biological Resource Centers (BRCs) with a great importance in science, industry and education. Their objective is to preserve the purity, viability and genomic integrity of every single strain as a member of such collection. Since improvement of molecular methods nowadays brought many novel approaches in manipulation with strains of microorganisms, they can also be useful for characterization of existing stored strains. ITS1 region in nuclear DNA is preferred barcoding marker for taxon identification, whi

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Yim, Won Cheol, and John C. Cushman. "Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments." PeerJ 5 (June 22, 2017): e3486. http://dx.doi.org/10.7717/peerj.3486.

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Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent ye

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Lorenzo, Consuelo, Jorge E. Bolaños-Citalán, and Oscar G. Retana-Guiascón. "Rediscovery of Heteromys nelsoni in its type locality after over a century." Mammalia 84, no. 1 (December 18, 2019): 6–9. http://dx.doi.org/10.1515/mammalia-2018-0154.

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Abstract We rediscovered a population of Nelson’s spiny pocket mouse (Heteromys nelsoni; Merriam, 1902) in the type locality of Pinabeto in the Mexican state of Chiapas, 121 years after it was last collected. We describe five topotype specimens according to their morphology and external measurements, and we confirm its identity at the species level in the Basic Local Alignment Search Tool (BLAST) of GenBank. As the population of H. nelsoni in Pinabeto is isolated, it is likely to be susceptible to extinction. There is a need to carry out additional scientific studies of this microendemic speci

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Tian, Hongling, Xiaoshuang Xu, Fusheng Zhang, Yaoqin Wang, Shuhong Guo, Xuemei Qin, and Guanhua Du. "Analysis ofPolygala tenuifoliaTranscriptome and Description of Secondary Metabolite Biosynthetic Pathways by Illumina Sequencing." International Journal of Genomics 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/782635.

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Radix polygalae, the dried roots ofPolygala tenuifoliaandP. sibirica, is one of the most well-known traditional Chinese medicinal plants. Radix polygalae contains various saponins, xanthones, and oligosaccharide esters and these compounds are responsible for several pharmacological properties. To provide basic breeding information, enhance molecular biological analysis, and determine secondary metabolite biosynthetic pathways ofP. tenuifolia, we applied Illumina sequencing technology and de novo assembly. We also applied this technique to gain an overview ofP. tenuifoliatranscriptome from samp

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Goldberg, Michael, Michelle Wei, Benjamin Tycko, Inna Falikovich та Dorothy Warburton. "Identification and expression analysis of the human μ-protocadherin gene in fetal and adult kidneys". American Journal of Physiology-Renal Physiology 283, № 3 (1 вересня 2002): F454—F463. http://dx.doi.org/10.1152/ajprenal.00012.2002.

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We recently cloned μ-protocadherin, a developmentally regulated cell adhesion molecule that contains an extracellular region with four cadherin-like ectodomains and a triply repeating mucin domain in its longer isoform. Expression of μ-protocadherin in L929 cells resulted in cellular aggregation, confirming its role in intercellular adhesion. We now identify the human μ-protocadherin ortholog and study its distribution in vivo and its targeting in polarized epithelia. Basic Local Alignment Search Tool searches and fluorescent in situ hybridization analysis on the basis of human-mouse synteny r

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Lau, Joann M., and David L. Robinson. "Effectiveness of a Cloning and Sequencing Exercise on Student Learning with Subsequent Publication in the National Center for Biotechnology Information GenBank." CBE—Life Sciences Education 8, no. 4 (December 2009): 326–37. http://dx.doi.org/10.1187/cbe.09-05-0036.

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With rapid advances in biotechnology and molecular biology, instructors are challenged to not only provide undergraduate students with hands-on experiences in these disciplines but also to engage them in the “real-world” scientific process. Two common topics covered in biotechnology or molecular biology courses are gene-cloning and bioinformatics, but to provide students with a continuous laboratory-based research experience in these techniques is difficult. To meet these challenges, we have partnered with Bio-Rad Laboratories in the development of the “Cloning and Sequencing Explorer Series,”

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FLORES FERNÁNDEZ, JOSÉ MIGUEL, CARLA PATRICIA BARRAGÁN ÁLVAREZ, CARLA VANESSA SÁNCHEZ HERNÁNDEZ, EDUARDO PADILLA CAMBEROS, CELIA GONZÁLEZ CASTILLO, DANIEL ORTUÑO SAHAGÚN, and MOISÉS MARTÍNEZ VELÁZQUEZ. "Molecular characterization and expression analysis of three novel autophagy-related genes from the cattle tick Rhipicephalus (Boophilus) microplus (Acari: Ixodidae)." Parasitology 143, no. 13 (September 9, 2016): 1802–9. http://dx.doi.org/10.1017/s0031182016001542.

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SUMMARYThe cattle tick Rhipicephalus (Boophilus) microplus is a hematophagous ectoparasite of major importance for the livestock industry. It shows a remarkable ability to survive over long periods without feeding. However, the mechanisms used to endure long-term starvation are poorly understood. It is believed that autophagy, a process of intracellular protein degradation, may play a significant role to confront adverse environmental conditions. To advance our understanding of autophagy in R. microplus, in the present study we report the molecular characterization of three autophagy-related (

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Jancso, Mario A., Susana A. Sculaccio, and Otavio H. Thiemann. "Identification of sugarcane genes involved in the purine synthesis pathway." Genetics and Molecular Biology 24, no. 1-4 (December 2001): 251–55. http://dx.doi.org/10.1590/s1415-47572001000100033.

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Nucleotide synthesis is of central importance to all cells. In most organisms, the purine nucleotides are synthesized de novo from non-nucleotide precursors such as amino acids, ammonia and carbon dioxide. An understanding of the enzymes involved in sugarcane purine synthesis opens the possibility of using these enzymes as targets for chemicals which may be effective in combating phytopathogen. Such an approach has already been applied to several parasites and types of cancer. The strategy described in this paper was applied to identify sugarcane clusters for each step of the de novo purine sy

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Kim, Ok-Sun, Yong-Joon Cho, Kihyun Lee, Seok-Hwan Yoon, Mincheol Kim, Hyunsoo Na, Sang-Cheol Park, et al. "Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species." International Journal of Systematic and Evolutionary Microbiology 62, Pt_3 (March 1, 2012): 716–21. http://dx.doi.org/10.1099/ijs.0.038075-0.

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Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have

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Khatun, Marjia, and Laila Anjuman Banu. "A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient." European Journal of Medical and Health Sciences 3, no. 2 (March 31, 2021): 19–21. http://dx.doi.org/10.24018/ejmed.2021.3.2.744.

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A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardi

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Dwarka, Arvin, Cynthia M. Ross Friedman, Mairi E. MacKay, and Don Nelson. "Polymerase chain reaction identification of a female-specific genetic marker in Arceuthobium americanum (lodgepole pine dwarf mistletoe) and its implications for Arceuthobium sex determination." Botany 89, no. 6 (June 2011): 369–77. http://dx.doi.org/10.1139/b11-025.

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In North America, the most widespread and speciose mistletoe is Arceuthobium M. Bieb. (dwarf mistletoes, Viscaceae), which is a dioecious parasite of conifers. Little is known about its sex determination system, and sex chromosomes have not been identified. A genetic marker for early gender discrimination in Arceuthobium would be useful in the study of sex ratios and sex determination. Here, random amplified polymorphic DNA analysis via the polymerase chain reaction (PCR) was used to investigate genetic differences between genders in Arceuthobium americanum Nutt. ex Engelm. collected near Kaml

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Kolondam, Beivy Jonathan. "Evaluasi Deteksi Berbasis PCR untuk Bakteri Bifidobacterium longum dalam Sampel Feses Bayi dari Kota Manado." JURNAL ILMIAH SAINS 20, no. 1 (April 6, 2020): 18. http://dx.doi.org/10.35799/jis.20.1.2020.27702.

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Bifidobakteria merupakan mikroflora yang umum hidup dalam usus manusia sejak bayi. Peran Bifidobacterium longum yang positif sebagai salah satu bakteri yang menunjang kesehatan inangnya membuat bakteri ini menjadi objek studi yang menarik. Salah satu instrumen dalam penelitian adalah adalah metode deteksi bakteri B. longum yang berbasis PCR (Polymerase Chain Reaction) gen 16S rRNA. Dengan mempertimbangkan bahwa perancangan primer untuk deteksi ini sudah lebih dari 20 tahun, penelitian ini bertujuan mengevaluasi hasil deteksi melalui PCR terhadap B. longum dalam feses bayi. Akurasi hasil diliha

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Maynes, Jason T., Richard G. Yuan, and Floyd F. Snyder. "Identification, Expression, and Characterization of Escherichia coli Guanine Deaminase." Journal of Bacteriology 182, no. 16 (August 15, 2000): 4658–60. http://dx.doi.org/10.1128/jb.182.16.4658-4660.2000.

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ABSTRACT Using the human cDNA sequence corresponding to guanine deaminase, the Escherichia coli genome was scanned using the Basic Local Alignment Search Tool (BLAST), and a corresponding 439-residue open reading frame of unknown function was identified as having 36% identity to the human protein. The putative gene was amplified, subcloned into the pMAL-c2 vector, expressed, purified, and characterized enzymatically. The 50.2-kDa protein catalyzed the conversion of guanine to xanthine, having a Km of 15 μM with guanine and a k cat of 3.2 s−1. The bacterial enzyme shares a nine-residue heavy me

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Capelja, Eleonora, Nevena Stevic, Vladislava Galovic, Milana Novakovic, and Maja Karaman. "rDNA based analysis of autochtonous fungal species from Serbia." Genetika 46, no. 1 (2014): 33–42. http://dx.doi.org/10.2298/gensr1401033c.

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Determination of fungal species by traditional morphological approach can often be problematic. In the phylum Basidiomycota, sporocarps of different species can share very similar morphoanatomical characteristics. Using molecular markers and phylogenetic species concept this problem can be reduced. In this study identification of six autochtonous fungal species, collected from several locations in Serbia (Tara, Kopaonik, Stara planina) was done by comparison between morphological and molecular data of fungal species, as well as information obtained from phylogenetic tree. ITS sequences amplifi

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Hajibaba, Majid, Mohsen Sharifi, and Saeid Gorgin. "The Influence of Memory-Aware Computation on Distributed BLAST." Current Bioinformatics 14, no. 2 (January 7, 2019): 157–63. http://dx.doi.org/10.2174/1574893613666180601080811.

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Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worke

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Odronic, Shelley I., Thomas Scheidemantel, Marion J. Tuohy, Deborah Chute, Gary W. Procop, and Christine N. Booth. "Two Cases of Cokeromyces recurvatus in Liquid-Based Papanicolaou Tests and a Review of the Literature." Archives of Pathology & Laboratory Medicine 136, no. 12 (December 1, 2012): 1593–96. http://dx.doi.org/10.5858/arpa.2011-0493-cr.

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We present 2 cases of Cokeromyces recurvatus in routine, liquid-based Papanicolaou tests (ThinPrep). Patient 1 is a healthy, asymptomatic, 26-year-old woman with no pertinent past medical history. Patient 2 is a healthy, asymptomatic, 47-year-old woman with no pertinent past medical history. The Papanicolaou tests from both patients showed many fungal-like elements as globose, yeastlike forms measuring 10 to 30 µm in diameter with multiple, narrowly attached apparent “daughter” buds. This morphology was consistent with Paracoccidioides brasiliensis. However, broad-range fungal polymerase chain

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Kong, Liang, Lingfu Kong, and Rong Jing. "Improving the Prediction of Protein Structural Class for Low-Similarity Sequences by Incorporating Evolutionaryand Structural Information." Journal of Advanced Computational Intelligence and Intelligent Informatics 20, no. 3 (May 19, 2016): 402–11. http://dx.doi.org/10.20965/jaciii.2016.p0402.

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Protein structural class prediction is beneficial to study protein function, regulation and interactions. However, protein structural class prediction for low-similarity sequences (i.e., below 40% in pairwise sequence similarity) remains a challenging problem at present. In this study, a novel computational method is proposed to accurately predict protein structural class for low-similarity sequences. This method is based on support vector machine in conjunction with integrated features from evolutionary information generated with position specific iterative basic local alignment search tool (

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Toledo, Bethânia Figueiredo Barbosa de, Jackson Marcondes, and Eliana Gertrudes de Macedo Lemos. "Caracterização de rizóbios indicados para produção de inoculantes por meio de sequenciamento parcial do 16S rRNA." Pesquisa Agropecuária Brasileira 44, no. 4 (April 2009): 384–91. http://dx.doi.org/10.1590/s0100-204x2009000400008.

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O objetivo deste trabalho foi confrontar as sequências parciais do gene 16S rRNA de estirpes padrão de rizóbios com as de estirpes recomendadas para a produção de inoculantes no Brasil, com vistas à verificação da confiabilidade do sequenciamento parcial desse gene para a identificação rápida de estirpes. Foram realizados sequenciamentos através de reação em cadeia da polimerase (PCR) com iniciadores relativos à região codificadora do gene 16S rRNA entre as bactérias estudadas. Os resultados foram analisados pela consulta de similaridade de nucleotídeos aos do "Basic Local Alignment Search Too

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Valli S, Abiraami, and Mythili T. "BIOINFORMATIC STUDY OF AN ANTITUMOR PROTEIN, AZURIN." Asian Journal of Pharmaceutical and Clinical Research 11, no. 6 (June 7, 2018): 169. http://dx.doi.org/10.22159/ajpcr.2018.v11i6.23339.

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Objective: The main objective of this study is to analyze the structure and function of an antitumor protein, azurin, thereby giving validation to the protein structure and existing physicochemical properties in the anticancer protein which are responsible for the anticancer activity.Methods: Protein sequence analysis was done using Basic Local Alignment Search Tool (BLAST) with ten different randomly selected species of Pseudomonas obtained from GenBank. The physicochemical properties, prediction of secondary structure, identification of motifs and domains, three-dimensional (3-D) structure o

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Shiels, Browne, Donovan, Murray, and Saha. "Molecular Characterization of Twenty-Five Marine Cyanobacteria Isolated from Coastal Regions of Ireland." Biology 8, no. 3 (August 7, 2019): 59. http://dx.doi.org/10.3390/biology8030059.

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Twenty-five marine cyanobacteria isolated from Irish coasts were characterized based on their morphological characters and 16S rRNA gene sequence analysis. In addition, superoxide dismutase (SOD) and malate dehydrogenase (MDH) isoenzyme banding patterns were used to differentiate two morphologically ambiguous isolates. In this study, six new cyanobacteria-specific primers were designed, and a 16S rRNA gene of twenty-five morphologically diverse cyanobacteria was successfully PCR amplified (1198–1396 bps). Assembled 16S rRNA sequences were used both for a basic local alignment search tool (BLAS

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Amosova, Alexandra V., Lilit Ghukasyan, Olga Yu Yurkevich, Nadezhda L. Bolsheva, Tatiana E. Samatadze, Svyatoslav A. Zoshchuk, and Olga V. Muravenko. "Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families." Plants 10, no. 6 (May 30, 2021): 1105. http://dx.doi.org/10.3390/plants10061105.

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The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and c

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Rosa, Sarah Brena Aparecida, Bárbara Guimarães Csordas, Sandra Maria do Valle Leone de Oliveira, Amanda Ribeiro dos Santos, Anamaria Mello Miranda Paniago та James Venturini. "Prediction of Conserved Peptides of Paracoccidioides for Interferon-γ Release Assay: The First Step in the Development of a Lab-Based Approach for Immunological Assessment during Antifungal Therapy". Journal of Fungi 6, № 4 (19 грудня 2020): 379. http://dx.doi.org/10.3390/jof6040379.

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Impaired antigen-specific cell-mediated immunity (CMI) is a primary immunological disturbance observed in individuals that develop paracoccidioidomycosis (PCM) after exposure to Paracoccidioides spp. Restoration of Paracoccidioides-specific CMI is crucial to stop the antifungal treatment and avoid relapses. A convenient and specific laboratory tool to assess antigen specific CMI is required for the appropriate clinical treatment of fungal infections, in order to decrease the time of antifungal therapy. We used an interferon-γ release assay strategy, used in the diagnosis of latent tuberculosis

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