Open WHO coronavirus updates

Latest sequence work in progress ---- see also: repeats observed on this version

covid-5ync Merci de visiter le site covid-5ync covid-5ync est une application d'asssitance aux biotechnologistes dans leurs travaux en cours en réponse à la crise de coronavirus covid-19. Cette contribution vise à associer la communauté de développeurs dans les travaux de lutte contre l'épidémie. Merci de transmettre vos suggestions et demandes de support à covid5yn@5ync.net Votre participation est bienvenue et appréciée! Thank you for visiting covid-5ync project web site. covid-5ync, a DNA analysis assistant application, is our modest contribution to help biotechnology engineers in their effort to defeat the covid-19 epidemic. Its main goal is to associate the IT community's collaboration in this new human challenge. Please send your suggestions and support requests to covid5yn@5ync.net Your participation is greatly welcome and appreciated! Install application application's click-once setup page page d'installation click-once de l'application Source code application's source code respository (github) code source de l'applicaton sur github Taoffi's Blog About the project, .NET, databases, and mobile technologies. à propos du projet, .NET, les bases de données et autres sujets.

App change log ========================== THE FUTURE OF THIS APP: ========================== We aim to integrate in biotechnology research environement. Many tools are already out there. Our goal is to integrate their services and data into this app. We are working on a few near-future targets: * Connect to NCBI databases and services to use their great features and let you join other research projects * Structuring application data for interoperability with common research environments + Handle various sequences' formats either online or offline to receive or transmit data * Build an application local databases for managing your sequences information as libraries ========================== -------------------------- 2020-03-17 -------------------------- * optimized search process (much faster, work in progress to do better) * corrected initial search region end index (was limited to 255!) * updated online sequence with latest repeats -------------------------- 2020-03-15 -------------------------- * structured application data to save and reload work sessions (retreive back your previous session analysis: regions, repeats, hairpins...) * application file now saved in xml format (extension = .covid-5ync) * better search for repeats and hairpins (other optimizations under work) * better user interface for managing sequence and regions info * default embedded sequence set to NCBI MT163719 29903bp RNA linear VRL 10-MAR-2020 * sequence file with ongoing analysis can be loaded at http://covid-5.5ync.net/covid19-work-in-progress.xml -------------------------- 2020-03-13 -------------------------- * added feature: user managed favorite web sites => menu Bookmarks/favorites * fixed some update issues with repeats and search collections -------------------------- 2020-03-12 -------------------------- * edit sequence name and summary (on start main window) * define and managae named regions: define start / end coordinates, name and summary. locate region on sequence set region as main search region for repeat search * warn on load new sequence if pending changes - yes!... that is not yet perfect. just a first step preparing for library management! * better property change notification on new sequence -------------------------- 2020-03-11 -------------------------- * edit sequence name and summary (future use for saving/loading sequences) * edit found search fragments' name and info (for search, repeats, pair-repeats) * individually clear search baskets * added link to NCBI SARS web site (File menu) -------------------------- 2020-03-08 -------------------------- * define search region (for repeats/hairpins/primers) from 1st contigous selection * search for pair-repeats (future feature: hairpins needs more settings) * search (and pair-search) strings from text file (one string per line): work in progress: check source text * reset selection to found repeats * save or copy pair-repeats to file or to clipboard -------------------------- 2020-03-07 -------------------------- - settings: repeats and primers. currently only repeat settings are used - search for repeats: that is a lengthy process that can run in the background. you can also choose to visually show current repeat search position on the sequence (see Tools / Settings). we are working for enhancing the process. any advice is greatly welcome -:) - search process optimized - save repeats to clipboard / to file - corrected reading UPPER CASE nucleotide files -:) - some more visual ui enhancements -------------------------- 2020-03-05 -------------------------- Added Application Menus * open sequence file * save sequence to file * load / reload built-in sequence (covid-19 sequence embedded into the application: source ncbi) * copy selected regions to clipboard: * save selected regions to file ====================== HOW TO SELECT SEQUENCE REGIONS ====================== ** click node = start selection (cancels all previous selections) ** shift+click regions end = region selection end ** ctrl+click node = add new region selection ** ctrl+shift+click node = end new region selection * Goto Covid-19 NCBI page * Contact us => send mail -------------------------- 2020-03-04 -------------------------- - calculate sequence melting temperature (enhanced Baldino-based) - use shortcuts: * ctrl + f = search * alt + f = search complementary - new feature: selection basket (found search fragments) - sequence stats: show nucleotide percentage - copy selected fragments (with starting coordinates) to clipboard (shortcut: crl+c) -------------------------- 2020-02-29 -------------------------- The current (beta) version is a start point in a work in progress: * The covid-19 DNA sequence is loaded on application startup * You can view, zoom-in / out (using Ctrl + mouse wheel) * You can search the sequence for nucleotides OR complementary pairs. =============================

Some screen captures

Search and pair-search

Menus

Named regions / repeats / pair-repeats

70 repeats observed on 2020-03-17 sequence (length range = 8 -16 nucleotides)