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Multiple alignment program for amino acid or nucleotide sequences

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  • Clustering huge protein sequence sets in linear time.
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Luciphor2 re-implements the original Luciphor algorithm 9see above in JAVA and expands it to work on any post-translational modification. It can also read in tab-delimited files with scores from any protein search tool. Bioinformatics, It aggregates data from multiple experiments, adjusts spectral counts to accurately account for peptides shared across multiple proteins, and performs common normalization steps. It can also output the spectral count data at the gene level, thus simplifying the integration and comparison between gene and protein expression data.

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Abacus is compatible with the widely used Trans-Proteomic Pipeline suite of tools and comes with a graphical user interface making it easy to interact with the program. The main aim of Abacus is to streamline the analysis of spectral count data by providing an automated, easy to use solution for extracting this information from proteomic data sets for subsequent, more sophisticated statistical analysis.

Proteomcis, Features a hierarchical model with predictive recursive algorithm.

DNA, Chromosomes, Genes, and Traits: An Intro to Heredity

Includes percentile normalization and multiple threading for fast computing. Proteomics, Software for the analysis of differential protein expression using label-free spectral count data.


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The hierarchical model of QSPEC pools statistical information for mean and variance estimates across all proteins in the presence of limited number of replicate data. In a typical quantitative proteomics experiment, there are rarely a sufficient number of replicates to render conventional statistic-based tests such as T-test applicable. QSPEC addresses this problem and calculates the ratio of likelihoods Bayes Factor for differential expression for each protein based on certain model assumptions Poisson-family distributions for count data and Gaussian distribution for intensity data.

A biclustering method for constructing protein complexes using filtered high-confidence interaction data from label-free quantitative AP-MS experiment. The method forms bait clusters based on the similarity of quantitative interaction profiles as anchors of protein complexes, and identifies submatrices of prey proteins showing consistent quantitative association within the anchor bait clusters.

The statistical model here determines the optimal number of bait clusters and prey clusters in the data, automatically yielding the configuration of highly probable protein complexes.

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Molecular Systems Biology, We developed core components of the widely used open source data analysis pipeline Trans-Proteomic Pipeline, TPP for primary processing of mass spectrometry-based proteomic data. MSFragger : ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics MSFragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.

Philosopher : A complete toolkit for shotgun proteomics data analysis Philosopher provides easy access to third-party tools and custom algorithms allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated protein reports.