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# Basic Local Aligment Search Tool

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A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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... Protein−ligand complexes were prepared with the Protein Preparation Wizard [45] to fix protonation states of amino acids, add hydrogens, and fix missing side-chain atoms. The template structures for homology modeling were identified using BLAST [46], and microtubule affinity . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...
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... Iterative sequence similarity searches using PSI-BLAST were executed for each NUP subunit type (24,43). PSI-BLAST runs reported herein were performed using the non-redundant protein database (nr) and the Entrez Query 'NOT fragment NOT partial', to exclude protein fragments or partial proteins and keep only complete sequences, avoiding low quality or ambiguous information. ...
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... To identify a template structure that we could use as a reference to generate a 3D model of AQP3, we ran a BLAST [55] on UniProt with the blosum62 matrix. The PDB structure showing the highest amino acid sequence identity with AQP3 (50.2%) was the one with PDB id equal to 6F7H from AQP10 [56]. ...
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The natural polyphenolic compound Rottlerin (RoT) showed anticancer properties in a variety of human cancers through the inhibition of several target molecules implicated in tumorigenesis, revealing its potential as an anticancer agent. Aquaporins (AQPs) are found overexpressed in different types of cancers and have recently emerged as promising pharmacological targets. Increasing evidence suggests that the water/glycerol channel aquaporin-3 (AQP3) plays a key role in cancer and metastasis. Here, we report the ability of RoT to inhibit human AQP3 activity with an IC50 in the micromolar range (22.8 ± 5.82 µM for water and 6.7 ± 2.97 µM for glycerol permeability inhibition). Moreover, we have used molecular docking and molecular dynamics simulations to understand the structural determinants of RoT that explain its ability to inhibit AQP3. Our results show that RoT blocks AQP3-glycerol permeation by establishing strong and stable interactions at the extracellular region of AQP3 pores interacting with residues essential for glycerol permeation. Altogether, our multidisciplinary approach unveiled RoT as an anticancer drug against tumors where AQP3 is highly expressed providing new information to aquaporin research that may boost future drug design.
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The rapid identification of Influenza A virus and its variants, which cause severe respiratory diseases, is imperative to providing timely treatment and improving patient outcomes. Conventionally, two separate assays (total test duration of up to 6 h) are required to initially differentiate Influenza A and B viruses and subsequently distinguish the pdm H1N1 and H3N2 serotypes of Influenza A virus. In this study, we developed a multiplex real-time RT-PCR method for simultaneously detecting Influenza A and B viruses and subtyping Influenza A virus, with a substantially reduced test duration. Clinical specimens from hospitalized patients and outpatients with influenza-like symptoms in Eastern Taiwan were collected between 2011 and 2015, transported to Hualien Tzu Chi Hospital, and analyzed. Conventional RT-PCR was used to subtype the isolated Influenza A viruses. Thereafter, for rapid identification, the multiplex real-time RT-PCR method was developed and applied to identify the conserved regions that aligned with the available primers and probes. Accordingly, a multiplex RT-PCR assay with three groups of primers and probes (MAF and MAR primers and MA probe; InfAF and InfAR primers and InfA probe; and MBF and MBR primers and MB probe) was established to distinguish these viruses in the same reaction. Thus, with this multiplex RT-PCR assay, Influenza B, Influenza A pdm H1N1, and Influenza A H3N2 viruses were accurately detected and differentiated within only 2.5 h. This multiplex RT-PCR assay showed similar analytical sensitivity to the conventional singleplex assay. Further, the phylogenetic analyses of our samples revealed that the characteristics of these viruses were different from those reported previously using samples collected during 2012-2013. In conclusion, we developed a multiplex real-time RT-PCR method for highly efficient and accurate detection and differentiation of Influenza A and B viruses and subtyping Influenza A virus with a substantially reduced test duration for diagnosis.
... Sequences identified as telomeres were discarded, and sequences identified as ORFs, structural RNAs and nonconserved sequences; target motifs along with 300 bp of flanking sequences on each side were recovered and saved in a local database set. Each sequence was then aligned to all genomes of the Ustilaginales taxon group available on April 30, 2019, using blastn option of BLAST [40] software of NCBI. The highest-scoring single loci conserved in all organisms were sought, and 21 candidates were obtained. ...
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Mathematical methods for comparison of nucleic acid sequences are reviewed. There are two major methods of sequence comparison: dynamic programming and a method referred to here as the regions method. The problem types discussed are comparison of two sequences, location of long matching segments, efficient database searches and comparison of several sequences.
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A new development is introduced here in the use of dynamic programming in finding pattern similarities in genetic sequences, as was first done by Needleman and Wunsch (1969). A condition of pattern similarity is defined and an algorithm is given which scans any set of similarities and screens out those which fail to meet the condition. When the set to be scanned contains every pair of segments, one from each of two given sequences of lengthsm andn (i.e. every possible location for a pattern similarity), then it completes the scan in a number of computational steps proportional tom·n, leaving those pairs of segments which satisfy the similarity condition. The algorithm is based on the concept of match density, as suggested by Goad and Kanehisa (1982).
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