Evaluates protein activity. VIPER can transform low-depth single cell RNA-Seq (scRNA-Seq) profiles into highly reproducible protein activity profiles. It underlines cell state and allows users to delete technical artifacts and batch effects. This tool permits investigation of critical lineage markers and can serve to deduce differential protein activity. It is useful for the analysis of single cell biology.
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.
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.
Aims to detect protein matches against signatures from the PROSITE database, a resource that contains large collection of biologically meaningful signatures. ScanProsite is a web application that offers several online functionalities: (1) detection of intra-domain biological features, (2) a new graphical result representation and (3) an interactive result viewer.
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.
Allows users to create data sets of protein sequences. UniqueProt algorithm is a way to thin out some set of sequences by removing bias originating from redundancy without losing the most important representatives. This software removes bias of sequence-redundant proteins from a given data set in the hope of acquiring unique sub-sets that constitute more accurate approximations to the goal of analysing sets representative for the protein universe.
Identifies kinase activating mutations from a combination of sequence and structural information. Kinact is a machine learning-based predictive model implemented as a web server. It provides a set of analyses to help users investigate in detail the impact of the mutation. It uses graph-based signatures, sequence and structural data. This method also displays information on the group of homologue protein kinases according to the Standard Kinase Classification Scheme.
Predicts domain targets based on experimental screening result. MOTIPS is a program that first scans the target proteome by using the normalized position specific scoring matrix (PSSM) and then generates a hit list of potential domain targets. This approach employs two different ways to normalize the input data: the first one is designed for signal data from experiments; and the second one is designed for peptide data from experiments.
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.
Detects bioactive peptides within a protein sequence. PeptideLocator makes use of the likelihood that protein sequences are bioactive to process. This software can be utilized as part of a targeted identification pipeline for food peptides with beneficial properties such as antimicrobial peptides. It can identify bioavailable peptides from common food or proteins by combining cleavage patterns with the bioactivity prediction feature.
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.
Provides a method for ancestral sequence rebuilding for phylogenetically and biologically distinct taxa. SubRecon is a standalone application based on a merging of joint and marginal approaches. It is able to consider large datasets and can be applied to nucleotide, codon or amino acid states as well as for investigating multiple sites in parallel. In addition, users can parameter the output files and the computing threads.
Allows construction of solution adapted to proteomics data analysis. ViPDAC is a program that utilizes Amazon Web Services to analyze proteomics data. Users have to log into one of Amazon’s servers to use the ViPDAC interface, and pick an existing set of parameters or configure a new analysis. Once the analysis is done, it will save the results into a file available in downloading for users.
Allows users to build personalized protein databases (PPDs) using variant calls from next-generation genomic sequencing (NGS) data. GenPro was applied to the study of allelic-specific protein (ASP) abundance in human brain. It demonstrates that it is suitable to use PPDs in standard search algorithms. This tool assumes each base called have the same probability of being correct by imposing probability threshold for every base called.
Allows discovery of maximum independent sets. Leaf was applied to generate non-redundant sets from the PDB, using various sequence similarity and structure quality parameters, and several genomes. It identifies cliques in the graph that satisfy the criterion of having at least one vertex which is not connected to any vertex outside of the clique.
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.
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.
Provides a time-domain method that analyzes time-series omics datasets with high-level noise and possible decay. MICOP is a maximal information coefficient (MIC)-based module that permits users to identify and characterize oscillating molecules in omics datasets. It detects and characterizes oscillations in time-resolved omics data sets. It is also compatible with noisy data obtained with a low sampling frequency.
Allows users to specify any motif and the associated binding domain. DoReMi is a web application that includes the protein-protein association data into the scoring schema, allowing the extension of the usage from being a subsequently applied filter to a factor for ranking found potential instances. Moreover, this program can be applied for determining binding partners for PDZ domains.
Determines swapping phenomenon into a targeted protein sequence. 3Dswap-pred is a platform developed, based on a classifier that exploits the Random forest method, to detect 3D domain swapping from a FASTA file. The application can also be employed for assessing and qualifying putative members that plays a role in the phenomenon. It aims to extend the data available for crystallization experiments.