Basic Local Alignment Sequencing Tool (BLAST) is a bioinformatics tool used for analyzing nucleotide sequences with regards to their similarity. BLAST can be found online on biological databases such as the National Center for Biotechnology Information (NCBI) and other such repositories. The mechanism of BLAST allows the target sequence to be compared with other sequences to find regions of local similarity, and thus, a comparability quotient that determines the resemblance between the sequences is created. Due to the open-platform nature of the online databanks, several sequences can be accepted with little to no interjections regarding the quality of sequence submitted. An example of unclean nucleotide sequences can be based on the number of non-template nucleotides, denoted as "N," present within the sequence. Here we develop a self-established nucleotide sequence reading program known as "DNAChecker," which helps identify the quality of the target sequence and therefore proposes the effectiveness of the BLAST result. DNAChecker is an inbuilt, program that runs on Python 3.4 and was implemented in the United States Agency for International Development (USAID) project conducted in Indonesia International Institute for Life Sciences. Although DNAChecker has proven to be useful, it has a lot of room for improvements, such as having a more objectively accurate means of differentiating between good and bad sequences. AbstrakPenggunaan Algoritma "DNA Checker" untuk Pengembangan Riset Bioinformatika. Basic Sequence Alignment Tool (BLAST) adalah aplikasi bioinformatika yang digunakan untuk menganalisis sekuens nukleotida sehubungan dengan pensejajarannya. BLAST dapat ditemukan secara daring di database biologis seperti Pusat Nasional untuk Informasi Bioteknologi (NCBI) dan repositori lainnya. Mekanisme BLAST memungkinkan sekuens target untuk dibandingkan dengan sekuens lain untuk menemukan daerah kesamaan lokal, dan dengan demikian, dapat menghasilkan perbandingan yang menentukan kemiripan antara sekuens. Karena sifat platform terbuka dari bank data daring, beberapa urutan dapat diterima dengan sedikit atau tanpa interupsi terkait kualitas urutan yang disampaikan. Contoh urutan nukleotida tidak baik dapat didasarkan pada jumlah nukleotida non-template, dilambangkan sebagai "N," yang hadir dalam urutan. Di sini kami mengembangkan program pembacaan urutan nukleotida yang dikenal sebagai "DNAChecker," yang membantu mengidentifikasi kualitas urutan target dan karenanya meningkatkan keefektifan hasil pencarian BLAST. DNAChecker adalah program inbuilt, yang berjalan pada Python 3.4 dan diimplementasikan di proyek Badan Pembangunan Internasional Amerika Serikat (USAID) yang dilaksanakan di Institut Bioscientia Internasional Indonesia. Meskipun DNAChecker terbukti bermanfaat, ia tetap seyogyanya ditingkatkan fiturnya, seperti memiliki cara yang lebih akurat secara obyektif untuk membedakan urutan yang baik dan buruk.
of drug resistant mutations. Several crystal structures of RT-NNI complexes determined at high resolution (Ren et al. 1995, Nature Struct. Bioi. 2, 303-308, Ren eta!, 1995 show NNis bind to a hydrophobic pocket in RT about lOA hom the polymerase catalytic site. Analyses of these crystal stmctures illustrate the mechanisms ofNNI resistance to be mainly a loss of stabilizing van der Waals contacts between the protein and the inhibitor. To dissect out the structural requirements for the design of a potent NNI, we have detem1ined the crystal structures of a series of HEPT analogues coveiing a wide range of potencies (Hopkins et al, J.Med. Chem., in press). These complex structures reveal conformational changes in the protein some of which correlate with the potencies of the HEPT analogues. The major determinant of increased potency is the improved ring stacking interactions between the 6-benzyl Iing of the inhibitors and Tyrl81. The conformational switching ofTyrlSl into its more exploitable position is caused by ste1ic interactions with the 5-position substituent on the pyiimidine ling. All tight binding NNis possess groups which throw this conformational switch. We present here several complex structures of E.Coli PNP with its substrates and substrate analogs. Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of puIine ribo or 2'-deoxyiibonucleosides to the purine and Iibose or 2-deoxyiibose-1-phosphate. The enzyme has been isolated from both eukaryotic and prokaryotic organisms and functions in the pmine salvage pathways. The human and bovine PNPs are specific for the 6-oxo-puiines and many of their analogs, and both are tiimers with identical subunits. E.Coli Pi\'P represents another class of PNP identified from va~ious sources, which is hexameiic,has no sequence similaJity with human and bovine PNPs and accepts both 6-amino and 6-oxopuiines as substrates. E.Coli PNP has a strikingly different active site and binding features to its substrates compa~·ed with that of mammalian PNPs. The phosphate binding site consists of backbone Gly20 and three a~·ginine residuesArg43 and Arg87 from one subunit and Arg24 from the neighboiing subunit. The three a~·ginine residue hold the phosphate to form a strong binding net a11d yet a~·e flexible enough to allow phosphate to initiate the nucleophilic attack due to the long a~·rns of a~·ginine residues. E. Coli PNP does not undergo a large conformational change during the enzymatic reaction like in the case of mammalian PNP. The seiine protease thrombin plays a central role in blood clotting with the most prominent function being the conversion of fibrinogen to fibiin in the later stages of the coagulation cascade. A Ja~·ge number of inhibitor-thrombin complexes have been studied by X-ray crystallography. Most of these inhibitors bind to one or the other of the S l-S3 subsites of the active site or the fibiinogen recognition exosite. Less is known of the binding at the S' subsites that involve substrate residues downstream from the point of cleavage...
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