Journal articles: 'Protein Sequence Analysis'

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Plasterer, Thomas N. "PROTEAN: Protein Sequence Analysis and Prediction." Molecular Biotechnology 16, no. 2 (2000): 117–26. http://dx.doi.org/10.1385/mb:16:2:117.

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Johri, Parul, Mala Trivedi, and Sujeet Pratap Singh. "Atom based Profiling and Functional Enrichment analysis of Aquaporins." Research Journal of Biotechnology 16, no. 10 (September 25, 2021): 75–77. http://dx.doi.org/10.25303/1610rjbt7577.

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Sequence analysis is a computational biology method to study protein sequences by comparing amino acids of one protein sequence with the other (residual level comparison). This study reveals a new concept of comparing protein sequences at their basic atomic level. Aquaporins from various origin were compared at their atomic level and the study revealed that all the aquaporin proteins have a closed range of 31.0% to 34.2% of carbon atoms irrespective of their origin and amino acid sequence. Further the protein interaction and functional enrichment analysis of AQP7 showed significant interaction with glycerol kinase and ATP-sensitive inward rectifier potassium channel protein. Our insilico analysis on aquaporin proteins exposed that nature tends to maintain the overall carbon atom composition in the proteins regardless of their amino acid sequence composition which could be further used for their classification. Also, the most highly interacting partners for AQPs are the potassium buffering channel proteins.

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Kumari, Uma, Aastha Tanwar, Jositta George, and Daityari Nayak. "NGS Analysis to Detect Mutation in Brain Tumor Diagnostic." International Journal for Research in Applied Science and Engineering Technology 11, no. 7 (July 31, 2023): 1394–402. http://dx.doi.org/10.22214/ijraset.2023.54895.

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Abstract: This study presents an integrated computational approach for analyzing protein sequences and their 3D structures. By leveraging the MMDB Macromolecular database, homologs of a protein sequence of interest are identified, and interactive visualization of their structural properties is provided. The computational alignment method, using BLASTP, allows for efficient determination of sequence similarities and identification of conserved regions among multiple protein sequences. COBALT is employed to refine sequence alignments and facilitate graphical analysis of sequence relationships. RASMOL, a computational analysis program, generates 2-D representations of protein-ligand complexes, enabling visual exploration of their interactions. ORF finder is used to identify coding regions in mRNA sequences, aiding in the prediction of protein-coding regions. The approach is applied to brain tumor diagnostics using human biological samples, exploring the structural properties of brain tumor-related proteins with the help of the 2RHU protein structure and PYMOL visualization software. Overall, this integrated computational framework offers a comprehensive toolkit for protein sequence analysis, structure visualization, and homology modeling, with potential applications in drug discovery, molecular biology, and medical diagnostics

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Reguant, Roc, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, and Nicholas Paul Gauthier. "AlignmentViewer: Sequence Analysis of Large Protein Families." F1000Research 9 (March 27, 2020): 213. http://dx.doi.org/10.12688/f1000research.22242.1.

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AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.

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Reguant, Roc, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, and Nicholas Paul Gauthier. "AlignmentViewer: Sequence Analysis of Large Protein Families." F1000Research 9 (October 15, 2020): 213. http://dx.doi.org/10.12688/f1000research.22242.2.

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AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families. The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space. The tool is directly accessible in web browsers without the need for software installation. It can handle protein families with tens of thousands of sequences and is particularly suitable for evolutionary coupling analysis, e.g. via EVcouplings.org.

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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 (October 20, 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 sequence of pPLA4 and the available DNA or translated sequences of the plasmids encoding pediocin AcH, pediocin PA-1, and coagulin, possibly indicating a different origin. In addition to the bacteriocin operon, sequence analysis of pPLA4 revealed the presence of two open reading frames (ORFs). ORF1 encodes a putative mobilization (Mob) protein that is homologous to the pMV158 superfamily of mobilization proteins. Highest sequence similarity occurred between this protein and the Mob protein of L. plantarum NCDO 1088. ORF2 encodes a putative replication protein that revealed low sequence similarity to replication proteins of plasmids pLME300 from Lactobacillus fermentum and pYIT356 from Lactobacillus casei. The immunity protein of plantaricin 423 contains 109 amino acids. Although plantaricin 423 shares high sequence similarity with the pediocin PA-1 operon, no cross-reactivity was recorded between the immunity proteins of plantaricin 423 and pediocin PA-1.

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Nekrasov, Alexei N., Yuri P. Kozmin, Sergey V. Kozyrev, Rustam H. Ziganshin, Alexandre G. de Brevern, and Anastasia A. Anashkina. "Hierarchical Structure of Protein Sequence." International Journal of Molecular Sciences 22, no. 15 (August 3, 2021): 8339. http://dx.doi.org/10.3390/ijms22158339.

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Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs remains an actual research area. Here, we propose a mathematical method for revealing the hierarchical organization of protein sequences. The method is based on the pentapeptide as a unit of protein sequences. Employing the frequency of occurrence of pentapeptides in sequences of natural proteins and a special mathematical approach, this method revealed a hierarchical structure in the protein sequence. The method was applied to 24,647 non-homologous protein sequences with sizes ranging from 50 to 400 residues from the NRDB90 database. Statistical analysis of the branching points of the graphs revealed 11 characteristic values of y (the width of the inscribed function), showing the relationship of these multiple fragments of the sequences. Several examples illustrate how fragments of the protein spatial structure correspond to the elements of the hierarchical structure of the protein sequence. This methodology provides a promising basis for a mathematically-based classification of the elements of the spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used to solve biotechnological and medical problems.

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Hansen, Scott G., Lisa I. Strelow, David C. Franchi, David G. Anders, and Scott W. Wong. "Complete Sequence and Genomic Analysis of Rhesus Cytomegalovirus." Journal of Virology 77, no. 12 (June 15, 2003): 6620–36. http://dx.doi.org/10.1128/jvi.77.12.6620-6636.2003.

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ABSTRACT The complete DNA sequence of rhesus cytomegalovirus (RhCMV) strain 68-1 was determined with the whole-genome shotgun approach on virion DNA. The RhCMV genome is 221,459 bp in length and possesses a 49% G+C base composition. The genome contains 230 potential open reading frames (ORFs) of 100 or more codons that are arranged colinearly with counterparts of previously sequenced betaherpesviruses such as human cytomegalovirus (HCMV). Of the 230 RhCMV ORFs, 138 (60%) are homologous to known HCMV proteins. The conserved ORFs include the structural, replicative, and transcriptional regulatory proteins, immune evasion elements, G protein-coupled receptors, and immunoglobulin homologues. Interestingly, the RhCMV genome also contains sequences with homology to cyclooxygenase-2, an enzyme associated with inflammatory processes. Closer examination identified a series of candidate exons with the capacity to encode a full-length cyclooxygenase-2 protein. Counterparts of cyclooxygenase-2 have not been found in other sequenced herpesviruses. The availability of the complete RhCMV sequence along with the ability to grow RhCMV in vitro will facilitate the construction of recombinant viral strains for identifying viral determinants of CMV pathogenicity in the experimentally infected rhesus macaque and to the development of CMV as a vaccine vector.

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Chang, P. C., M. L. Hsieh, J. H. Shien, D. A. Graham, M. S. Lee, and H. K. Shieh. "Complete nucleotide sequence of avian paramyxovirus type 6 isolated from ducks." Journal of General Virology 82, no. 9 (September 1, 2001): 2157–68. http://dx.doi.org/10.1099/0022-1317-82-9-2157.

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There are nine serotypes of avian paramyxovirus (APMV). Only the genome of APMV type 1 (APMV-1), also called Newcastle disease virus (NDV), has been completely sequenced. In this study, the complete nucleotide sequence of an APMV-6 serotype isolated from ducks is reported. The 16236 nt genome encodes eight proteins, nucleocapsid protein (NP), phosphoprotein (P), V protein, matrix protein (M), fusion protein (F), small hydrophobic (SH) protein, haemagglutinin–neuraminidase (HN) protein and large (L) protein, which are flanked by a 55 nt leader sequence and a 54 nt trailer sequence. Sequence comparison reveals that the protein sequences of APMV-6 are most closely related to those of APMV-1 (NDV) and -2, with sequence identities ranging from 22 to 44%. However, APMV-6 contains a gene that might encode the SH protein, which is absent in APMV-1, but present in the rubulaviruses simian virus type 5 and mumps virus. The presence of an SH gene in APMV-6 might provide a link between the evolution of APMV and rubulaviruses. Phylogenetic analysis demonstrates that APMV-6, -1, -2 (only the F and HN sequences were available for analysis) and -4 (only the HN sequences were available for analysis) all cluster into a single lineage that is distinct from other paramyxoviruses. This result suggests that APMV should constitute a new genus within the subfamily Paramyxovirinae.

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Kerim, Tursun, Nijat Imin, Jeremy J. Weinman, and Barry G. Rolfe. "Proteomic analysis reveals developmentally expressed rice homologues of grass group II pollen allergens." Functional Plant Biology 30, no. 8 (2003): 843. http://dx.doi.org/10.1071/fp03100.

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Three isoallergens of Ory s 2, homologues of grass group II pollen allergens, were identified from rice and characterised by proteome and immunochemical analyses. The N-terminal amino acid sequence profiles of three proteins on a 2-dimensional electrophoresis (2-DE) gel of rice pollen proteins matched 100% to the protein sequences encoded by three rice expressed sequence tags (ESTs). The deduced protein sequences from these ESTs share sequence identities of 41–43% with the protein sequences of the group II pollen allergens of different grasses, and sequence identity of 39% with the C-terminal portion of rice group I pollen allergens. Signal peptide sequences, which are similar to the leader peptides of other major pollen allergens, are also present in the deduced amino acid sequences. Polyclonal antibodies, produced in rabbits using Ory s 2 proteins purified by 2-DE, were used to investigate the developmental-stage- and tissue-specific expression of Ory s 2 by immunochemical analysis. Results of immunochemical experiments show that Ory s 2 proteins are expressed only at the late stage of pollen development and they do not have cross-reactivity with group II pollen allergens from some other common grasses.

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Irminger-Finger, I., R. A. Laymon, and L. S. Goldstein. "Analysis of the primary sequence and microtubule-binding region of the Drosophila 205K MAP." Journal of Cell Biology 111, no. 6 (December 1, 1990): 2563–72. http://dx.doi.org/10.1083/jcb.111.6.2563.

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We have sequenced cDNA clones encoding the Drosophila 205K microtubule-associated protein (MAP), a protein that may be the species specific homologue of mammalian MAP4. The peptide sequence deduced from the longest open-reading frame reveals a hydrophilic protein, which has basic and acidic regions that are similar in organization to mammalian MAP2. Using truncated forms of the 205K MAP, a 232-amino acid region could be defined that is necessary for microtubule binding. The amino acid sequence of this region shares no similarity with the binding motif of MAP2 or tau. We also analyzed several embryonic cDNA clones, which show the existence of differentially spliced mRNAs. Finally, we identified several potential protein kinase target sequences. One of these is distal to the microtubule-binding site and fits the phosphorylation consensus sequence of proteins phosphorylated by the mitosis specific protein kinase cdc2. Our data suggest that the 205K MAP uses a microtubule-binding motif unlike that found in other MAPs, and also raise the possibility that the activities of the 205K MAP may be regulated by alternative splicing and phosphorylation.

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Jenvey, C. J., D. Alenizi, F. Almasi, C. Cairns, A. Holmes, S. Sloan, and M. J. Stear. "Bioinformatic analysis of eosinophil activity and its implications for model and target species." Parasitology 147, no. 4 (December 16, 2019): 393–400. http://dx.doi.org/10.1017/s0031182019001768.

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AbstractEosinophils are important immune cells that have been implicated in resistance to gastrointestinal nematode (GIN) infections in both naturally and experimentally infected sheep. Proteins of particular importance appear to be IgA-Fc alpha receptor (FcαRI), C-C chemokine receptor type 3 (CCR3), proteoglycan 3 (PRG3, major basic protein 2) and EPX (eosinophil peroxidase). We used known human nucleotide sequences to search the ruminant genomes, followed by translation to protein and sequence alignments to visualize differences between sequences and species. Where a sequence was retrieved for cow, but not for sheep and goat, this was used additionally as a reference sequence. In this review, we show that eosinophil function varies among host species. Consequently, investigations into the mechanisms of ruminant immune responses to GIN should be conducted using the natural host. Specifically, we address differences in protein sequence and structure for eosinophil proteins.

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ESKIN, ELEAZAR, and SAGI SNIR. "INCORPORATING HOMOLOGUES INTO SEQUENCE EMBEDDINGS FOR PROTEIN ANALYSIS." Journal of Bioinformatics and Computational Biology 05, no. 03 (June 2007): 717–38. http://dx.doi.org/10.1142/s0219720007002734.

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Statistical and learning techniques are becoming increasingly popular for different tasks in bioinformatics. Many of the most powerful statistical and learning techniques are applicable to points in a Euclidean space but not directly applicable to discrete sequences such as protein sequences. One way to apply these techniques to protein sequences is to embed the sequences into a Euclidean space and then apply these techniques to the embedded points. In this work we introduce a biologically motivated sequence embedding, the homology kernel, which takes into account intuitions from local alignment, sequence homology, and predicted secondary structure. This embedding allows us to directly apply learning techniques to protein sequences. We apply the homology kernel in several ways. We demonstrate how the homology kernel can be used for protein family classification and outperforms state-of-the-art methods for remote homology detection. We show that the homology kernel can be used for secondary structure prediction and is competitive with popular secondary structure prediction methods. Finally, we show how the homology kernel can be used to incorporate information from homologous sequences in local sequence alignment.

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Farinha, Mark A., and Andrew M. Kropinski. "Overexpression, purification, and analysis of the c1 repressor protein of Pseudomonas aeruginosa bacteriophage D3." Canadian Journal of Microbiology 43, no. 3 (March 1, 1997): 220–26. http://dx.doi.org/10.1139/m97-030.

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A 3.1-kb region of the bacteriophage D3 genome which contains the immunity functions has recently been sequenced (GenBank accession No. L22692). Sequence analysis indicated the presence of a putative repressor gene (c1) whose protein product functions to maintain the bacteriophage genome as a stably integrated prophage in the chromosome of Pseudomonas aeruginosa. A plasmid was constructed that overexpresses repressor C1 protein under control of Ptac in Escherichia coli. C1 protein was subsequently purified and characterized as a 223 amino acid protein with specific binding affinity for 14-base imperfect palindromic operator sequences located on the genome of bacteriophage D3. N-terminal protein sequence data obtained from automated Edman degradation (16 cycles) of purified repressor protein were identical to the predicted sequence based on DNA sequence analysis of the c1 open reading frame.Key words: promoter, repressor, operator, lambdoid phage, Pseudomonas aeruginosa.

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Day, A. A., C. I. McQuillan, J. D. Termine, and M. R. Young. "Molecular cloning and sequence analysis of the cDNA for small proteoglycan II of bovine bone." Biochemical Journal 248, no. 3 (December 15, 1987): 801–5. http://dx.doi.org/10.1042/bj2480801.

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The cDNA for the full-length core protein of the small chondroitin sulphate proteoglycan II of bovine bone was cloned and sequenced. A 1.3 kb clone (lambda Pg28) was identified by plaque hybridization with a previously isolated 1.0 kb proteoglycan cDNA clone (lambda Pg20), positively identified previously by polyclonal and monoclonal antibody reactivity and by hybrid-selected translation in vitro [Day, Ramis, Fisher, Gehron Robey, Termine & Young (1986) Nucleic Acids Res. 14, 9861-9876]. The cDNA sequences of both clones were identical in areas of overlap. The 360-amino-acid-residue protein contains a 30-residue propeptide of which the first 15 residues are highly hydrophobic. The mature protein consists of 330 amino acid residues corresponding to an Mr of 36,383. The core protein contains three potential glycosaminoglycan-attachment sites (Ser-Gly), only one of which is within a ten-amino-acid-residue homologous sequence seen at the known attachment sites of related small proteoglycans. Comparisons of the published 24-residue N-terminal protein sequence of bovine skin proteoglycan II core protein with the corresponding region in the deduced sequence of the bovine core protein reveals complete homology. Comparison of the cDNA-derived sequences of bovine bone and human embryonic fibroblast proteoglycans shows a hypervariable region near the N-terminus. Nucleotide homology between bone and fibroblast core proteins was 87% and amino acid homology was 90%.

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HIRANO, Hisashi. "Amino Acid Sequence Analysis by Gas-Phase Protein Sequencer." Journal of Japan Oil Chemists' Society 38, no. 10 (1989): 791–99. http://dx.doi.org/10.5650/jos1956.38.791.

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Guerrucci, Marie-Anne, and Robert Bellé. "Characterisation of protein structure/function relationship by sequence analysis without previous alignment: Distinction between sub-groups of protein kinases." Bioscience Reports 15, no. 3 (June 1, 1995): 161–71. http://dx.doi.org/10.1007/bf01207456.

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Using an approach for protein comparison by computer analysis based on signal treatment methods without previous alignment of the sequence, we have analysed the structure/function relationship of related proteins. The aim was to demonstrate that from a few members of related proteins, specific parameters can be obtained and used for the characterisation of newly sequenced proteins obtained by molecular biology techniques. The analysis was performed on protein kinases, which comprise the largest known family of proteins, and therefore allows valid estimations to be made. We show that using only a dozen defined proteins, the specific parameters extracted from their sequences classified the protein kinase family into two sub-groups: the protein serine/threonine kinases (PSKs) and the protein tyrosine kinases (PTKs). The analysis, largely involving computation, appears applicable to large scale data-bank analysis and prediction of protein functions.

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Yang, Lina, Pu Wei, Cheng Zhong, Zuqiang Meng, Patrick Wang, and Yuan Yan Tang. "A Fractal Dimension and Empirical Mode Decomposition-Based Method for Protein Sequence Analysis." International Journal of Pattern Recognition and Artificial Intelligence 33, no. 11 (October 2019): 1940020. http://dx.doi.org/10.1142/s0218001419400202.

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In bioinformatics, the biological functions of proteins and their interactions can often be analyzed by the similarity of their sequences. In this paper, the authors combine the fractal dimension, empirical mode decomposition (EMD), and sliding window for protein sequence comparison. First, the protein sequence is characterized and digitized into a signal, and then the signal characteristics are obtained by using EMD and fractal dimension. Each protein sequence can be decomposed into Intrinsic Mode Functions (IMFs). The fixed window’s fractal dimension is applied to each IMF and the original signal to extract the protein sequence characteristics. Experiments have shown that the feature extracted by this hybrid method is superior to the EMD method alone.

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Barna, J. "DNA and Protein Sequence Analysis." Journal of Medical Genetics 34, no. 11 (November 1, 1997): 959–60. http://dx.doi.org/10.1136/jmg.34.11.959-a.

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Rost, Burkhard, and Alfonso Valencia. "Pitfalls of protein sequence analysis." Current Opinion in Biotechnology 7, no. 4 (August 1996): 457–61. http://dx.doi.org/10.1016/s0958-1669(96)80124-8.

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Aebersold, Ruedi. "Solid-phase protein sequence analysis." Nature 343, no. 6255 (January 1990): 291–92. http://dx.doi.org/10.1038/343291a0.

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Combet, C., C. Blanchet, C. Geourjon, and G. Deléage. "NPS@: Network Protein Sequence Analysis." Trends in Biochemical Sciences 25, no. 3 (March 2000): 147–50. http://dx.doi.org/10.1016/s0968-0004(99)01540-6.

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Smith, CA. "Methods in Protein Sequence Analysis." Biochemical Education 18, no. 1 (January 1990): 54–55. http://dx.doi.org/10.1016/0307-4412(90)90036-n.

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Seabrook, BN. "Methods in protein sequence analysis." Biochemical Education 22, no. 1 (January 1994): 59. http://dx.doi.org/10.1016/0307-4412(94)90193-7.

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Sass, Philip M. "DNA AND PROTEIN SEQUENCE ANALYSIS." Shock 8, no. 2 (August 1997): 156. http://dx.doi.org/10.1097/00024382-199708000-00021.

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Light, Albert. "Methods of protein sequence analysis." Analytical Biochemistry 167, no. 1 (November 1987): 210. http://dx.doi.org/10.1016/0003-2697(87)90153-9.

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Wittmann-Liebold, B. "High-sensitive protein sequence analysis." Pure and Applied Chemistry 64, no. 4 (January 1, 1992): 537–43. http://dx.doi.org/10.1351/pac199264040537.

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Szopa, J. "Expression analysis of a Cucurbita cDNA encoding endonuclease." Acta Biochimica Polonica 42, no. 2 (June 30, 1995): 183–89. http://dx.doi.org/10.18388/abp.1995_4643.

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The nuclear matrices of plant cell nuclei display intrinsic nuclease activity which consists in nicking supercoiled DNA. A cDNA encoding a 32 kDa endonuclease has been cloned and sequenced. The nucleotide and deduced amino-acid sequences show high homology to known 14-3-3 protein sequences from other sources. The amino-acid sequence shows agreement with consensus sequences for potential phosphorylation by protein kinase A and C and for calcium, lipid and membrane-binding sites. The nucleotide-binding site is also present within the conserved part of the sequence. By Northern blot analysis, the differential expression of the corresponding mRNA was detected; it was the strongest in sink tissues. The endonuclease activity found on DNA-polyacrylamide gel electrophoresis coincided with mRNA content and was the highest in tuber.

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Milburn, D., R. A. Laskowski, and J. M. Thornton. "Sequences annotated by structure: a tool to facilitate the use of structural information in sequence analysis." Protein Engineering Design and Selection 11, no. 10 (October 1, 1998): 855–59. http://dx.doi.org/10.1093/protein/11.10.855.

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Mruk, Karen, Brian M. Farley, Alan W. Ritacco, and William R. Kobertz. "Calmodulation meta-analysis: Predicting calmodulin binding via canonical motif clustering." Journal of General Physiology 144, no. 1 (June 16, 2014): 105–14. http://dx.doi.org/10.1085/jgp.201311140.

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The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM–peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator to this meta-analysis resulted in a tool that identifies potential CaM-binding domains within a given sequence. To allow users to search for CaM-binding motifs within a protein of interest, perform the meta-analysis, and then compare the results to target peptide–CaM structures deposited in the Protein Data Bank, we created a website and online database. The availability of these tools and analyses will facilitate the design of CaM-related studies of ion channels and membrane transport proteins.

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Anashkina, Anastasia A., Irina Yu Petrushanko, Rustam H. Ziganshin, Yuriy L. Orlov, and Alexei N. Nekrasov. "Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization." Entropy 23, no. 12 (December 7, 2021): 1647. http://dx.doi.org/10.3390/e23121647.

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Background: Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units. Methods: We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues—“information unit”. The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences. Results: The developed mathematical apparatus gives stable results on the structural unit description even with a significant variation in the parameters. The optimal length of the information unit is five, and the number of allowed substitutions is one. Examples of the application of the method for the design of protein molecules, intermolecular interactions analysis, and the study of the mechanisms of functioning of protein molecular machines are given. Conclusions: ANIS method makes it possible not only to analyze native proteins but also to design artificial polypeptide chains with a given spatial organization and, possibly, function.

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Tanaka, A., C. P. Gibbs, R. R. Arthur, S. K. Anderson, H. J. Kung, and D. J. Fujita. "DNA sequence encoding the amino-terminal region of the human c-src protein: implications of sequence divergence among src-type kinase oncogenes." Molecular and Cellular Biology 7, no. 5 (May 1987): 1978–83. http://dx.doi.org/10.1128/mcb.7.5.1978-1983.1987.

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We sequenced the 5'-coding region of the human c-src gene, exons 2 through 5, corresponding to one-third of the human c-src protein consisting of 536 amino acids. Sequence analysis of the src type of protein kinases revealed that the amino-terminal region encoded by exon 2 contains sequences specific for the src proteins and raised the possibility that this region is involved in the recognition of a src-specific substrate(s) or receptor(s).

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Tanaka, A., C. P. Gibbs, R. R. Arthur, S. K. Anderson, H. J. Kung, and D. J. Fujita. "DNA sequence encoding the amino-terminal region of the human c-src protein: implications of sequence divergence among src-type kinase oncogenes." Molecular and Cellular Biology 7, no. 5 (May 1987): 1978–83. http://dx.doi.org/10.1128/mcb.7.5.1978.

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We sequenced the 5'-coding region of the human c-src gene, exons 2 through 5, corresponding to one-third of the human c-src protein consisting of 536 amino acids. Sequence analysis of the src type of protein kinases revealed that the amino-terminal region encoded by exon 2 contains sequences specific for the src proteins and raised the possibility that this region is involved in the recognition of a src-specific substrate(s) or receptor(s).

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Bailey, J. M., M. Rusnak, and J. E. Shively. "Compact Protein Sequencer for the C-Terminal Sequence Analysis of Peptides and Proteins." Analytical Biochemistry 212, no. 2 (August 1993): 366–74. http://dx.doi.org/10.1006/abio.1993.1342.

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Reznikoff, William S., Seth R. Bordenstein, and Jennifer Apodaca. "Comparative Sequence Analysis of IS50/Tn5 Transposase." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8240–47. http://dx.doi.org/10.1128/jb.186.24.8240-8247.2004.

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ABSTRACT Comparative sequence analysis of IS50 transposase-related protein sequences in conjunction with known structural, biochemical, and genetic data was used to determine domains and residues that play key roles in IS50 transposase function. BLAST and ClustalW analyses have been used to find and analyze six complete protein sequences that are related to the IS50 transposase. The protein sequence identity of these six homologs ranged from 25 to 55% in comparison to the IS50 transposase. Homologous motifs were found associated with each of the three catalytic residues. Residues that play roles in transposase-DNA binding, protein autoregulation, and DNA hairpin formation were also found to be conserved in addition to other residues of unknown function. On the other hand, some homologous sequences did not appear to be competent to encode the inhibitor regulatory protein. The results were also used to compare the IS50 transposase with the more distantly related transposase encoded by IS10.

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Xia-Yun, Jiang, Zou Shu-Ming, and Zhou Pei-Gen. "Cloning and sequence analysis of complete cDNA of chitin deacetylase from Mucor racemosus." Chinese Journal of Agricultural Biotechnology 4, no. 2 (August 2007): 167–72. http://dx.doi.org/10.1017/s1479236207001489.

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AbstractA complete chitin deacetylase (CDA) complementary DNA (cDNA) from Mucor racemosus was cloned and sequenced by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification cDNA end (RACE) with gene special conserved primers. The cDNA sequence was submitted to GenBank (DQ538514). The complete cDNA with full-length of 1506 bp contained a 67 bp 5′-untranslated region, an open reading frame of 1344 bp and 95 bp 3′-untranslated region including tailing site AATAAA. The gene encoded a sequence of 448 amino acid residues and consisted of core nucleotides encoding a polysaccharide deacetylase domain covering 32% of the entire sequence. The CDA gene shared sequence homology with those of several fungi. The corresponding homology of the deduced amino acid sequences varied from 21 to 69%. Phylogenetic analysis according to the deduced amino acid sequences matched the classical fungi taxonomy. The three-dimensional structure of this protein was predicted. The protein had a whole CDA functional domain and a polysaccharide deacetylase domain.

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Clouthier, Sharon C., Trent Rector, Nathan E. C. Brown, and Eric D. Anderson. "Genomic organization of infectious salmon anaemia virus." Journal of General Virology 83, no. 2 (February 1, 2002): 421–28. http://dx.doi.org/10.1099/0022-1317-83-2-421.

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The RNA genome segment order, nucleotide sequence and the putative encoded proteins were determined for infectious salmon anaemia virus (ISAV). Eight segments of genomic viral RNA between 1·0 and 2·4 kb in length were identified. RNA segments 1–6 each had a predicted single open reading frame encoding the P1, PB1, NP, P2, P3 and HA proteins, respectively. Segment 7 encoded the P4/P5 proteins and segment 8 encoded the P6/P7 proteins. Seven virion proteins with molecular masses between 25 and 72 kDa were found by SDS–PAGE analysis. The 72 and 42 kDa proteins were immunoreactive with ISAV antiserum from Atlantic salmon. The molecular mass of the 72 kDa virion protein suggested that it was the NP protein encoded by segment 3. The amino acid sequence was conserved, sharing 96·6% identity with the NP protein of a Scottish ISAV isolate. Comparison of the amino acid sequences obtained by N-terminal analyses and cDNA nucleotide translation revealed that the 42 and 47 kDa proteins were the HA and P3 proteins encoded by segments 6 and 5, respectively. In addition, analysis provided evidence for their protein synthesis initiation sites. Like the HA protein, the signal sequence and potential glycosylation sites of P3 suggested that it was a surface glycoprotein. The predicted amino acid sequence shared 83·1, 84·0 and 99·6% identity to the predicted P3 protein sequences for ISAV isolates from Norway, Scotland and Maine, respectively. These results establish the specificity, migration, number and nucleotide sequence of the eight RNA segments of the ISAV genome.

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Karlin, S., and G. Ghandour. "Comparative statistics for DNA and protein sequences: single sequence analysis." Proceedings of the National Academy of Sciences 82, no. 17 (September 1, 1985): 5800–5804. http://dx.doi.org/10.1073/pnas.82.17.5800.

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39

Karlin, S., and G. Ghandour. "Comparative statistics for DNA and protein sequences: multiple sequence analysis." Proceedings of the National Academy of Sciences 82, no. 18 (September 1, 1985): 6186–90. http://dx.doi.org/10.1073/pnas.82.18.6186.

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40

Fan-Yun, Lin, Hu Yin-Gang, Song Guo-Qi, Zhang Hong, Liu Tian-Ming, and He Bei-Ru. "Isolation and analysis of genes induced by rehydration after serious drought in broomcorn millet (Panicum miliaceum L.) by SSH." Chinese Journal of Agricultural Biotechnology 3, no. 3 (December 2006): 237–42. http://dx.doi.org/10.1079/cjb2006119.

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AbstractIn order to investigate the molecular mechanism of rehydration after serious drought in broomcorn millet (Panicum miliaceum L.), a forward subtracted cDNA library was constructed between normal watered leaves and rehydrated leaves after serious drought conditions, using the suppressive subtraction hybridization (SSH) technique. A total of 60 positive clones were picked out at random from the subtracted library and sequenced, and redundancy sequences were removed after sequence alignment. Based on the results of sequence homologous comparison and function querying, 32 expressed sequence tags (EST) were highly homologous with known ESTs. Most of those sequences were related to either abiotic or biotic stress in plants. Of those sequences, 11 ESTs were homologous with ESTs in rat (Rattus norvegicus) liver after partial hepatectomy. The Blast result of proteins revealed that 28 ESTs were similar to known proteins. The functions of these proteins mainly involve signal transduction, transcription and protein processing. This experiment demonstrated that a range of specific genes was induced and expressed in broomcorn millet during the rehydration stage after serious drought.

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41

Buckley, K. M., E. Floor, and R. B. Kelly. "Cloning and sequence analysis of cDNA encoding p38, a major synaptic vesicle protein." Journal of Cell Biology 105, no. 6 (December 1, 1987): 2447–56. http://dx.doi.org/10.1083/jcb.105.6.2447.

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We have isolated from a lambda gt11 rat brain cDNA library cDNA clones encoding greater than 95% of the open reading frame and untranslated regions of the mRNA for p38, the most abundant of the integral membrane proteins of the synaptic vesicle. Phage containing cDNA that encoded vesicle proteins were identified by screening fusion proteins with a polyclonal serum to rat brain synaptic vesicles. To identify phage carrying p38 sequences, fusion proteins were used to affinity purify monospecific antibodies from the original heterogeneous serum; antibodies to a 38,000-D protein were then identified by Western blotting. Inserts carrying DNA-encoding p38 sequences were subcloned into plasmid vectors and used to generate cDNA probes for Northern blot analysis. A major transcript of 2.4 kb was expressed specifically in brain and endocrine tissue but not in liver, consistent with the tissue-specific expression of the protein detected by antibody techniques. Using three overlapping clones that encoded fusion proteins, we identified and sequenced approximately 85% of the cDNA. Two additional Eco RI fragments at the 5' end of the mRNA were obtained from a fourth clone identified by screening a second lambda gt11 library with a 5' cDNA probe. The cDNA encoded an open reading frame of 298 amino acids with a 3' untranslated region of 1.4 kb. The protein shares no sequence homology with other Ca2+-binding proteins. The availability of a cDNA clone for an integral synaptic vesicle protein should facilitate studies of its function in transmitter release, its intracellular targeting, and regulation of synaptic vesicle biogenesis during development and regeneration of nerve terminals.

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McDermott, Jason E., Paul Bruillard, Christopher C. Overall, Luke Gosink, and Stephen R. Lindemann. "Prediction of multi-drug resistance transporters using a novel sequence analysis method." F1000Research 4 (March 9, 2015): 60. http://dx.doi.org/10.12688/f1000research.6200.1.

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There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.

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McDermott, Jason E., Paul Bruillard, Christopher C. Overall, Luke Gosink, and Stephen R. Lindemann. "Prediction of multi-drug resistance transporters using a novel sequence analysis method." F1000Research 4 (May 29, 2015): 60. http://dx.doi.org/10.12688/f1000research.6200.2.

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There are many examples of groups of proteins that have similar function, but the determinants of functional specificity may be hidden by lack of sequence similarity, or by large groups of similar sequences with different functions. Transporters are one such protein group in that the general function, transport, can be easily inferred from the sequence, but the substrate specificity can be impossible to predict from sequence with current methods. In this paper we describe a linguistic-based approach to identify functional patterns from groups of unaligned protein sequences and its application to predict multi-drug resistance transporters (MDRs) from bacteria. We first show that our method can recreate known patterns from PROSITE for several motifs from unaligned sequences. We then show that the method, MDRpred, can predict MDRs with greater accuracy and positive predictive value than a collection of currently available family-based models from the Pfam database. Finally, we apply MDRpred to a large collection of protein sequences from an environmental microbiome study to make novel predictions about drug resistance in a potential environmental reservoir.

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Barton, Geoffrey J. "Protein Sequence Alignment Techniques." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1139–46. http://dx.doi.org/10.1107/s0907444998008324.

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The basic algorithms for alignment of two or more protein sequences are explained. Alternative methods for scoring substitutions and gaps (insertions and deletions) are described, as are global and local alignment methods. Multiple alignment techniques are explained, including methods for profile comparison. A summary is given of programs for the alignment and analysis of protein sequences, either from sequence alone, or from three-dimensional structure.

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Kristensen, T., R. A. Wetsel, and B. F. Tack. "Structural analysis of human complement protein H: homology with C4b binding protein, beta 2-glycoprotein I, and the Ba fragment of B2." Journal of Immunology 136, no. 9 (May 1, 1986): 3407–11. http://dx.doi.org/10.4049/jimmunol.136.9.3407.

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Abstract We report here a partial primary structure for human complement protein H. Tryptic peptides comprising 27% of the H molecule were isolated by conventional techniques and were sequenced (333 amino acid residues). Several mixed-sequence oligonucleotide probes were constructed, based on the peptide sequence data, and were used to screen a human liver cDNA library. The largest recombinant plasmid (pH1050), which hybridized with two probes, was further characterized. The cDNA insert of this plasmid contained coding sequence (672 bp) for 224 amino acids of H. The 3' end of this clone had a polyadenylated tail preceded by a polyadenylation recognition site (ATTAAA) and a 3'-untranslated region (229 bp). Four regions of internal homology, each about 60 amino acids in length, were observed in the derived protein sequence from this cDNA clone, and a further seven from the tryptic peptide sequences. The consensus sequence for each of the repetitive units of H was four cysteines, two prolines, three glycines, one tryptophan, and two tyrosines/phenylalanines. Based on the mole percent values for each of these amino acids, it is likely that H is composed of about 20 repetitive units of this nature. Furthermore, the repetitive unit of H shows pronounced homology with the Ba fragment of B, the C4b binding protein, and beta 2-glycoprotein I. Therefore, it seems that at least portions of these proteins have evolved from a common ancestral DNA element.

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Saqi, Mansoor. "An analysis of structural instances of low complexity sequence segments." "Protein Engineering, Design and Selection" 8, no. 11 (1995): 1069–73. http://dx.doi.org/10.1093/protein/8.11.1069.

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Halaby, D. M., A. Poupon, and J. P. Mornon. "The immunoglobulin fold family: sequence analysis and 3D structure comparisons." Protein Engineering, Design and Selection 12, no. 7 (July 1999): 563–71. http://dx.doi.org/10.1093/protein/12.7.563.

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Kaur, Navjot, Rajbir Singh Cheema, and Harmandeep Singh Harmandeep Singh. "Multiple Sequence Alignment and Profile Analysis of Protein Family Utsing Hidden Markov Model." International Journal of Scientific Research 2, no. 6 (June 1, 2012): 208–11. http://dx.doi.org/10.15373/22778179/june2013/66.

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Ghozlane, Amine, Agnel Praveen Joseph, Aurelie Bornot, and Alexandre G. de Brevern. "Analysis of protein chameleon sequence characteristics." Bioinformation 3, no. 9 (May 4, 2009): 367–69. http://dx.doi.org/10.6026/97320630003367.

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50

Kuhn, Alfred. "Methods in protein sequence analysis 1986." Journal of Chromatography A 410 (January 1987): 514. http://dx.doi.org/10.1016/s0021-9673(00)90090-6.

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Journal articles on the topic 'Protein Sequence Analysis'

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