Sequence alignment

Bài giảng Tin sinh học đại cương - Chương 3: Bắt cặp trình tự (Sequence Alignment) giới thiệu chung và tập trung làm rõ hiện tượng bắt cặp hai trình tự, bắt cặp nhiều trình tự. Bài giảng hữu ích với các bạn chuyên ngành Sinh học.

37p maiyeumaiyeu26 23-12-2016 186 29   Download

Chương này trình bày các kiến thức về quy hoạch động. Những nội dung chính trong chương này gồm có: Giới thiệu, giải quyết một số bài toán bằng quy hoạch động, bài tập, DP cho Sequence Alignment, hỏi đáp. Mời các bạn cùng tham khảo để biết thêm các nội dung chi tiết.

33p tangtuy12 02-06-2016 116 18   Download

Chương này gồm có những nội dung chính sau: Giới thiệu tóm tắt về dự án Human Genome; bài toán sequence alignment: Các vấn đề cần giải quyết, scoring system, lập trình động cho vấn đề pairwise alignment; bài toán local sequence alignment. Mời tham khảo.

32p tangtuy12 02-06-2016 111 7   Download

Lecture Algorithm design - Chapter 6: Dynamic programming II include all of the following: Sequence alignment, hirschberg's algorithm, Bellman-Ford algorithm, distance vector protocols, negative cycles in a digraph.

50p youcanletgo_03 14-01-2016 36 3   Download

Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware present a new approach to accelerat- ing MAFFT on Graphics Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) programming model. Compared with the implementations of other MSA algorithms on GPUs, parallelization of MAFFT is more challenging since the space complexity.

14p ducla78 30-07-2015 47 5   Download

The plant enzyme phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) shows homology to histidine ammonia-lyase (HAL) whose structure has been solved by X-ray crystallography. Based on amino-acid sequence alignment of the two enzymes, mutagenesis was performed on amino-acid residues that were identical or similar to the active site residues in HAL to gain insight into the importance of this residues in PAL for substrate binding or catalysis. We mutated the following amino-acid residues: S203, R354, Y110, Y351, N260, Q348, F400, Q488 and L138....

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In the biosynthesis of the antiarrhythmic alkaloid ajmaline, polyneuridine aldehyde esterase (PNAE) catalyses a central reaction by transforming polyneuridine aldehyde into epivellosimine, which is the immediate precursor for the synthesis of the ajmalane skeleton. The PNAE cDNA was previously heterologously expressed in E. coli. Sequence alignments indicated that PNAE has a 43% identity to a hydroxynitrile lyase from Hevea brasiliensis, which is a member of the a/b hydrolase superfamily. The catalytic triad, which is typical for this family, is conserved.

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Manganese lipoxygenase was isolated to homogeneity from the take-all fungus, Gaeumannomyces graminis. The C-terminal amino acids and several internal peptides were sequenced, and the information was used to obtain a cDNA probe by RT/PCR. Screening of a genomic library of G. graminis yielded a full-length clone of the Mn-Lipoxygenase gene. cDNA analysis showed that the gene spanned 2.6 kb and contained one intron (133 bp). Northern blot analyses indicated two transcripts (2.7 and 3.1 kb). The deduced amino-acid sequence of the Mn-Lipoxygenase precursor (618 amino acids, 67.

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The Rv0948c gene fromMycobacterium tuberculosisH37Rv encodes a 90 amino acid protein as the natural gene product with chorismate mutase (CM) activity. The protein, 90-MtCM, exhibits Michaelis–Menten kinetics with akcat of 5.5 ± 0.2 s )1 and a Kmof 1500 ± 100lmat 37C and pH 7.5. The 2.0 A˚ X-ray structure shows that 90-MtCM is an alla-helical homodimer (Protein Data Bank ID: 2QBV) with the topology ofEscheri-chia coliCM (EcCM), and that both protomers contribute to each catalytic site.

12p research12 29-04-2013 38 3   Download

Limitedproteolysis of the pyruvate decarboxylase (E1,a2b2 ) component of the pyruvate dehydrogenase (PDH) multi-enzyme complexofBacillus stearothermophilushas indicated the importance for catalysis of a site (Tyr281-Arg282) in the E1asubunit (Chauhan, H.J., Domingo, G.J., Jung, H.-I. & Perham, R.N. (2000)Eur. J. Biochem.267, 7158–7169). This site appears to be conserved in the a-subunit of hetero-tetrameric E1s and multiple sequence alignments suggest that there are additional conserved amino-acid residues in this region, part of a common pattern with the consensus sequence -YR-H-D-YR-DE-.

10p tumor12 20-04-2013 54 3   Download

Inorganic pyrophosphatase (PPase) is an important enzyme that catalyzes the hydrolysis of inorganic pyro-phosphate (PPi)intoortho-phosphate (P i ). We report here the molecular cloning and characterization of a gene encoding the soluble PPase of the roundworm Ascaris suum. The predicted A. suumPPase consists of 360 amino acids with a molecular mass of 40.6 kDa and a pI of 7.1.

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Almost all protein database search methods use amino acid substitution matrices for scoring, optimizing, and assessing the statistical significance of sequence alignments. Much care and effort has therefore gone into con-structing substitution matrices, and the quality of search results can depend strongly upon the choice of the proper matrix. A long-standing problem has been the comparison of sequences with biased amino acid composi-tions, for which standard substitution matrices are not optimal....

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Cytosolic 5¢-nucleotidase/phosphotransferase specific for 6-hydroxypurine monophosphate derivatives (cN-II), belongs to a class of phosphohydrolases that act through the formation of an enzyme–phosphate intermediate. Sequence alignment with members of the P-type ATPases/L-2-halo-acid dehalogenase superfamily identified three highly con-served motifs in cN-II and other cytosolic nucleotidases. Mutagenesis studies at specific amino acids occurring in cN-II conservedmotifswereperformed.

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The conduction of protons through human Nox2 has pre-viously been shown to be dependent upon His115. Align-ment of sequences for both animal and plant Nox proteins indicated that histidines 115 and 119 are both highly con-served, while His111 was conserved among animal homo-logues of Nox1–4. To investigate the possible role that these histidine residues might play in the conduction of protons through Nox2, we have introduced both paired and single mutations into these histidine residues.

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Spinocerebellar ataxia types 2 (SCA2) and 3 (SCA3) are autosomal-dominantly inherited, neurodegenerative dis-eases caused by CAG repeat expansions in the coding regions of the genes encoding ataxin-2 and ataxin-3, respectively. To provide a rationale for further functional experiments, we explored the proteinarchitectures of ataxin-2 and ataxin-3. Using structure-based multiple sequence alignments of homologous proteins, we investigated domains, sequence motifs, and interaction partners.

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Fifty-nine amino acid sequences belonging to family 57 (GH-57) of the glycoside hydrolases were collected using the CAZy server, Pfamdatabase andBLASTtools. Owing to the sequence heterogeneity of the GH-57 members, sequence alignments were performed using mainly manual methods. Likewise, five conserved regions were identified, which are postulated to be GH-57 consensus motifs.

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The Baeyer–Villiger monooxygenase (BVMO), 4-hydroxy-acetophenone monooxygenase (HAPMO), uses NADPH andO2 to oxidize a variety of aromatic ketones and sulfides. The FAD-containing enzyme has a 700-fold preference for NADPH over NADH. Sequence alignment with other BVMOs, which are all known to be selective for NADPH, revealed three conservedbasic residues,whichcouldaccount for the observed coenzyme specificity. The corresponding residues in HAPMO (Arg339, Lys439 and Arg440) were mutated and the properties of the purified mutant enzymes were studied. ...

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A homologue of interleukin 18 has been identified from rainbow trout,Oncorhynchus mykiss. The trout IL-18gene spans 3.7 kb and consists of six exons and five introns, sharing the same gene organization with its human coun-terpart. The putative translated protein is 199 amino acids in length with no predicted signal peptide. Analysis of the multiple sequence alignment reveals a conserved ICE cut site, resulting in a mature peptide of 162 amino acids. The trout IL-18 shares 41–45% similarity with known IL-18 molecules and contains an IL-1 family signature motif....

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In the postgenomic era it is essential that protein sequences are annotated correctly in order to help in the assignment of their putative functions. Over 1300 proteins in current pro-tein sequence databases are predicted to contain a PAS domainbaseduponaminoacid sequence alignments.Oneof theproblemswith the current annotationof thePASdomain is that this domain exhibits limited similarity at the amino acid sequence level.

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Placental protein 13 (PP13) was cloned from human term placenta. As sequence analyses, alignments and computa-tional modelling showed its conserved structural and func-tional homologyto members of the galectin family, the protein was designated galectin-13. Similar to human eosi-nophil Charcot–Leyden crystal protein/galectin-10 but not other galectins, its weak lysophospholipase activity was confirmed by 31 P-NMR. In this study, recombinant PP13/ galectin-13 was expressed and specific monoclonal antibody to PP13 was developed. ...

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