Search Results for "annotation"

An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). ...

The MITRE Annotation Toolkit (MAT) is a suite of tools which can be used for automated and human tagging of annotations. Annotation is a process, used mostly by researchers in natural language processing, of enhancing documents with information about the various phrase types the documents contain. MAT supports both UI interaction and command-line interaction, and provides various levels of control over the overall annotation process.

The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.

MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub repository: https://github.com/xiaoli-dong/metaerg

This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis.

pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..

Dasty is a web client for visualizing protein sequence feature information using DAS, the Distributed Annotation System.

To overcome current limitations in published MS data accessibility, we introduce a browser-based spectrum viewer that aims to allow exploration of alternative interpretations for MS spectra and additionally: can be operated by non-specialists, is open source, can be integrated into other software, gives appropriate publication-quality output. Spectrum Viewer is implemented totally on the client side using XHTML for menus and dialogs, SVG for spectrum and peptide display, and Javascript to...

BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.

A database of linguistic annotation of medical text (from MEDLINE), including corpora used with ABGene, BioCreative I and II, and the MedPost training corpus.

PhenoFam is a web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

BioNotate is an open-source web-based tool for the collaborative and distributed annotation of biomedical text with entities and facts of interest.

This project provides bookmarklet-based web page overlays based on recognized terms from vocabulary servers. These overlays can be used to assist users with unfamiliar terminology or can be used for annotation of web-based data and literature.

EuCAP is a web based tool and pipeline to that facilitates the submission of functional and structural community annotation to a genome annotation project.

The Patient and Sample System for Information Management (PASSIM) is a system for annotation and storage of data, associated with the collection of samples in biomedical studies.

PiAnoS is a powerful pedagogical web-interface developed by the University of Lausanne/School of Criminal Justice dedicated to the characteristics annotation made by forensic examiners on evidence and reference images during the individualization process