Protein identification and data analysis
Analysis of Mass Spectrometry. Data for Protein Identification. in Complex Biological Mixtures
... The current work opens several directions for future research. First, the al- gorithms discussed in chapters 3-5 take as input the results of database search which performs the crucial task of matching spectra to peptide ...
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Protein identification using MS/MS data
... 5. Site analysis For modifications that relate to biological function, the site of a modification can be just as important as the nature of the modification. If a peptide contains both modified and unmodi- fied ...
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Software for protein identification and quantitative analysis of mass spectrometry data used for protein characterization and proteomics Version 5.
... original data files, which prevents collisions in spectrum ...The identification levels are slightly lower when searching an MGF file versus searching the corresponding ....wiff data because ...
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Identification and analysis of a novel cysteine rich protein
... These data are consistent with cE13 promoting BMP signalling, but due to the relatively small number of the embryos exhibiting a decrease in the number of neural crest cells migrating from r4, this cannot be ...
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Protein Identification and Analysis Tools on the ExPASy Server
... the data to the ExPASy ...Tags Protein samples from 2-D gels can be submitted to Edman protein sequencing to create a sequence tag of three or four amino acids, after which the same protein ...
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Identification and analysis of potential targets in <em>Streptococcus sanguinis</em> using computer aided protein data analysis
... With an intention to avoid any cross-reactivity of the recognized drug with the human host, BlastP was performed alongside the 218 essential proteins and then the 81 nonhu- man homologue proteins having a threshold ...
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Computational identification and analysis of protein short linear motifs
... the data as a source of information to infer novel SLiMs is unrivalled ...of protein interaction ...central protein (hub) interacts with several interactors ...hub protein contains a module ...
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Protein Analysis and WEKA Data Mining
... and analysis of genetic data through data ...the identification of short amino-acid chains, which are included in families of related ...use data mining techniques stems from the sheer ...
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Development and assessment of scoring functions for protein identification using PMF data
... tification compares the masses of peptides derived from the experimental spectral peaks with each of the possible pep- tides generated by computationally digesting proteins in the sequence database. The MS/MS method ...
7
ProCAT: a data analysis approach for protein microarrays
... Functional protein microarrays often use only one color channel and, therefore, are especially prone to spatial arti- ...the identification of signifi- cant ...the protein chip and an inability to ...
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Identification of key lncRNAs in colorectal cancer progression based on associated protein–protein interaction analysis
... Methods Microarray data and data preprocessing Microarray data was downloaded from Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/) under the accession number GSE64857. This dataset ...
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Identification of novel prognostic indicators for triple-negative breast cancer patients through integrative analysis of cancer genomics data and protein interactome data
... the data itself and data quality we ...various data types, our method could achieve better predictive ...or analysis methods, thus we shall make efforts in our future work to provide a ...
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Identification and Analysis of Papillomavirus E2 Protein Binding Sites in the Human Genome
... mRNA analysis was carried out with SiHa and HaCaT cells 24 h after transfection with expression vectors for the low-risk HPV11 WT and N294A E2 proteins and high-risk HPV18 E2 ...
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omniCLIP: probabilistic identification of protein RNA interactions from CLIP seq data
... Here, we present omniCLIP, a probabilistic approach to identify regulatory elements from CLIP-data. Our model presents a principled framework for the analysis of RNA interaction assays and takes into ...
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Integrating domain similarity to improve protein complexes identification in TAP-MS data
... Algorithms introduced above have been developed based on topological features of PPI networks. However, due to experimental limitations, there exist false posi- tives and false negatives in PPIs. Besides physically ...
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Synthesis, identification and structure-activity relationship analysis of GATA4 and NKX2-5 protein-protein interaction modulators
... their protein −protein interactions are of pivotal importance in the regulation of biological ...SAR analysis of more than 200 structurally related compounds accompanied by a data ...
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Graph Theory Approaches to Protein Interaction Data Analysis
... PPI identification meth- ods, publicly available PPI data sets, some of the biological structures embedded in the PPI networks and methods used for their detection, and the currently known mathematical ...
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Identification of protein-protein and ribonucleoprotein complexes containing Hfq
... Characterizing protein-protein interactions is challenging in the case of Hfq since this protein is very abundant and has been found associated with ribosomes, DNA and RNA 6,7,43 ...Systematic ...
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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
... RNA-seq data from two ex- treme modalities of the phenotype, we were able to estab- lish a catalog of SNPs, stratify them by their impact on the protein sequence, and assess which SNPs had a signifi- cant ...
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The Analysis and Identification of Protein-coding Sequences for Yeast Using a Free Energy Model
... The protein-coding se- quences with longer minimum length have more reliably features as protein-coding sequences, which means a larger fraction of sequences can be correctly ...typical ...
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