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Unclassified software tools | Genome annotation

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AnoniMME
New
Serves for assuring anonymity to the Matchmaker Exchange (MME) platform with low overhead. AnoniMME enables anonymous queries within MME without enforcing any of its current security and functionality requirements. This tool is based on an information-theoretic approach and extends queries to support public key encryption of contact details. It exploits the underlying MME matching protocol and uses a public key provided to encrypt the match of the contact details of researchers.
Microcontax
Contains designed data sets based on a consensus taxonomy assignment among several data repositories. Microcontax is an R data package and a consensus taxonomy for prokaryotes designed to be the best possible for training taxonomic classifiers based on 16S rRNA sequence data. It offers functions for looking up higher-level taxonomy of specified genera. It also implements some ways to express uncertainties in the classifications, indicating if the input sequences are difficult to recognize.
myPhyloDB
A user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g., ANOVA, t-tests, linear regression, DESeq2, and PCoA) and normalization (rarefaction, DESeq2, proportion) tools for the comparative analysis of taxonomic abundance, species richness, and species diversity for projects of various types (e.g., human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired.
VaProS / VAriation effect on PROtein Structure and function
Integrates information in structural biology with genome, transcriptome, interactome and other information and provides seamless environment to scientists for analyzing these different types of information derived from different databases. The developers of VaProS aim to establish a core technology for drug discovery and other related fields in this country by providing a bird's-eye view of the whole data that assists a hypothesis (model) building process and by providing information manipulation environment that enables problem solving toward drug discovery and other related fields. VaProS is going to realize the aims above by integrating and disseminating the outcomes of the national projects in the related fields in the past to both structural biology and the whole life science discipline of not only academia, but industrial world as well.
GIMLET / Genome-wide Identification of Modulators using Local Energy statistical Test
New
Recognizes biological modulators of the complex gene regulation, such as combinatorial regulation, whether multiple transcription factors and modulators are functionally related. GIMLET can calculate all types of dependency, including non-monotonic and non-linear relationships, between random vectors in an arbitrary dimension. This tool can find genetic alterations and functional pertubagens modulating transcription factor activities.
simulatorZ
Simulates collections of independent genomic data sets, and performs training and validation with predicting algorithms. SimulatorZ is a package intended primarily to simulate collections of independent genomic data sets, as well as performing training and validation with predicting algorithms. It supports ExpressionSet and RangedSummarizedExperiment objects. It purposes functions to generate useful values from the true models for further analysis, to filter genes by Integrative Correlation and many others.
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