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Unclassified software tools | Protein sequence data analysis

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OOMPA / Object-Oriented Microarray and Proteomics Analysis
Provides several R packages for analysis of gene expression (RNA), proteomics profiling and other high-throughput molecular biology data. OOMPA can build object-oriented tools with consistent user interface. Among the different packages, SIBER assists for identifying bimodally expressed genes from next-generation RNAseq data. Another one, SuperCurve, classifies reverse-phase protein array (RPPA) with a generalized linear model and logistic function.
ProBias
Implements the BIAS algorithm to search a protein sequence for the instances of user-specified local and global compositional bias. ProBias is a web server whose interface consist of four parameters: the expected probability of each of the 20 amino acid types, the linkage distance, P-value cut-off and Sub-alphabet(s). The software can be combined with other de novo sequence analysis methods for guiding the search for potential functionally important sites or domains in novel proteins that lack functional annotation.
SeqFIRE / Sequence Feature and Indel Region Extractor
Enables the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices.
NetSurgeon
Recommends transcription factor (TF) deletions or over-expressions to move cells from an initial expression state to any desired state associated with any desired phenotype. NetSurgeon is an algorithm that can identify, given the expression profile of a cell in which a single TF has been deleted, this TF in a median of 22 predictions, whereas random guessing would take 161 tries. The software was applied to optimize yeast for ethanol production from glucose-xylose coculture.
DASS-GUI / Discovery of All Significant Substructures in Graphical Unit Interface
Enables usage of all discovery of all significant substructures (DASS) algorithms. DASS-GUI serves for pattern identification in non-sequence data with a largely overlapping range of applications. It works in two modes: (1) for calculation of closed sets (cs) and corresponding P-values; and (2) the analysis mode allowing additional filtering, calculation of cs hierarchy, calculation of means or standard deviations of different numerical features.
PINGU / PredIction of eNzyme catalytic residues usinG seqUence information
Assists users to perform catalytic residue predictions with improved precision by using physicochemical properties and evolutionary information from enzyme sequences. PINGU is construct around a support vector allowing to optimize the precision of the prediction. It attempts discrimination of catalytic residues with polarity index, position-specific scoring matrix (PSSM) and sequence conservation score. Moreover, users can use post-processing filter such as ligand binding residue information for obtaining precise predictions.
CryGetter
Aggregates Cry protein data, helping researchers of Bacillus thuringiensis and its Crystal proteins to deal with this data and allowing them to get all the relevant information for their work in a faster way compared to a manual protein data collection. CryGetter executes data retrieval and can perform automatic analysis of the protein alignments. It allows their users to generate more accurate results, since using it may prevent the error prone task of manually getting all the necessary data and processing them in various software to get the same result that the tool can generate in a unique automatic environment.
VarQ
Automatically analyzes several effects of SAS on protein function, particularly protein folding, activity, protein-protein interactions, and drug or cofactor binding. VarQ is a web application that includes features for selecting a critical set of representative structural configurations of the desired gene and diagnoses variants effect based on their impact. To perform, several properties are computed for each variant, including involvement in ligand binding, presence in the catalytic site, or the residue sidechain exposure to solvent.
CancerUBM / Cancer Urine BioMarkers
Detects urine peptide biomarkers, which can discriminate healthy controls from the oncological samples. CancerUBM employs the urine mass spectrometric data to proceed. It can be used to validate biomarkers for a variety of diseases and physiological changes. This tool includes models devoted to the analysis and prediction of oncological status from proteomics data. It provides three options to make its prediction: Mass-CE Spectra, Peptide Sequence and Protein Expression.
Webcutter
Helps restriction map nucleotide sequences. Webcutter is a free on-line tool with a simple, customizable interface, a worldwide platform-independent accessibility, a seamless interfaces to NCBI's GenBank, a DNA sequence database, and NEB's REBase, and a restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including the option of finding restriction sites that can be introduced into a sequence by silent mutagenesis ("silent cutters").
Protein Coverage Summarizer
Determines the percent of the residues in each protein sequence that have been identified. Protein Coverage Summarizer requires two input files: the first should contain the protein names and protein sequences (optionally with protein description) while the second should contain the peptide sequences and optionally also contain the protein name associated with each peptide sequence. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results. The results browser displays the protein sequences, highlighting the residues that were present in the peptide input file, and providing sequence coverage stats for each protein.
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