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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.


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.

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.

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.


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.