Search Results for "key"

The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can...

...According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. And since it uses pseudoalignment, it is robust to errors in the reads and preserves the key information needed for quantification. This makes kallisto not only fast but highly accurate as well. In many benchmarks, it even greatly outperforms existing tools.

The only open source counter to count any items the simplest and easiest way with the keyboard, or the mouse specifically on images. After associating a key to each item, or a predefined graphical symbol for images, pressing the key or clicking on the image increments its associated counter, and displays (for the images) the symbol at the mouse's pointer location. Such a project is so simple a child could use it!

PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently...

A key goal for NEMO is the development of a formal logic (“ontology”) to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, different experiment paradigms, and different modalities (EEG/MEG)

Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. ...

KAPPA (Key Aminoacid Pattern-based Protein Analyzer) is a sequence search program dedicated to the discovery and clustering of proteins defined by a key aminoacid pattern.

...The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175.

Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. ...

...Prokaryotic Proteogenomic Tool(PPT) is developed as a part of GenoSuite framework. PPT is for finding novel translations in prokaryotic genomes and is dependent on Mass Spectrometry based proteomics data and related genome sequence. Some Key features of the tool are.... (1) Configured for 4 open source algorithms to perform database searching for peptide identification. Any combination of the 4 algorithm can be chosen. (2) Lists out the genome search specific peptides(Novel peptides). (3) Spectral matches can be visualized for the quality assessment. (4) Lists out the novel proteins and changes in the existing protein annotations...

AutoMATRIX is a tool to predict key transcription factors in microarray experiments.

Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.

dna2abc turns DNA sequences into musical sequences. The key feature is the rule editor; a rule is a regular expression paired with a Tcl script. dna2abc scans a DNA sequence, testing each regular expression: if it matches, the Tcl script is run.