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/SigmoID

A Xojo/python tool for identification and annotation of transcription factor binding sites in bacterial genomes
  1. Xojo 89.7%
  2. HTML 7.5%
  3. Python 2.5%
  4. Other 0.3%
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Yevgeny Nikolaichik Yevgeny Nikolaichik
Yevgeny Nikolaichik and Yevgeny Nikolaichik Superpromoter extraction fixed 
A fix to a specific case when a CDS piece was extacted instead of the upstream regulatory region
Latest commit c12ad76 Apr 18, 2019
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Type Name Latest commit message Commit time
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Build_resources TomTom integrated into de novo pipeline Jan 11, 2019
Classes Load four plots via a file with paths to them Feb 10, 2019
Help Added protein seqs export Jun 9, 2016
Modules Superpromoter extraction fixed Apr 18, 2019
Pictures Improvements to de novo pipeline Dec 7, 2018
Pix Color preferences added Feb 13, 2018
Profiles Window localisations Jun 9, 2016
Python
TF_HMMs Filename problem fixed Feb 6, 2019
TF_families RegPrecise export improvements Oct 3, 2018
Toolbars
Windows Scan genome uses .sigs from RegPrecise Apr 11, 2019
.gitignore TF collections window update Sep 15, 2018
App.xojo_code Reverse complement profile Feb 3, 2019
Build Automation.xojo_code
CRtagBase Minor bug fixes Jan 29, 2019
CollectionStats.JSON
FileTypes.xojo_filetypeset Version 2 updates Oct 12, 2017
Genetic.codes Strand-specific and translation copying Mar 18, 2015
LICENSE Create LICENSE Jan 3, 2015
MainMenuBar.xojo_menu Reverse complement profile Feb 3, 2019
README.md Update README.md Jul 12, 2016
RegPreciseExport Minor bug fixes Jan 29, 2019
SigmoID.sh Browser improvements Apr 4, 2015
Sigmoid.xojo_project Scan genome uses .sigs from RegPrecise Apr 11, 2019
Sigmoid.xojo_resources Updates to de novo TFBS inference Aug 28, 2018
genomeStats.JSON RegPrecise improvements Sep 24, 2015

README.md

SigmoID is an application written in Xojo with important additions in python to ease annotation of sigma-factor and transcription factor binding sites in bacterial genome sequences. Functions:

  • visualise binding site alignments with sequence logo;
  • integrated access to RegPrecise and RegulonDB
  • extend, shorten and mask alignments;
  • create hmm profiles from alignments;
  • search bacterial genome sequences with calibrated (and uncalibrated) hmm profiles;
  • annotate promoters and transcription factor binding sites in GenBank-formatted genomes;
  • view regulatory sites in genomic context with the integrated genome browser;
  • view RNA-seq coverage data;
  • verify annotation via the integrated database search.

This version includes over 80 calibrated profiles optimised for (i) soft rot enterobacterial phytopathogens (Pectobacterium spp. and Dickeya spp.) and (ii) Pseudomonas spp.

The actual searches are done by nhmmer or mast which are included or could be configured to run from default installations on the user system.

Adding annotations to GenBank files and some other functions are implemented as python scripts, hence BioPython (version 1.64 and up) is required as well as 32-bit version of Python 2.7.x.

At the moment SigmoID is known to work on OS X (10.8 and up), 64-bit and 32-bit Linux distributions (Ubuntu 14.04 is tested for 64-bit and 12.04 for 32-bit) and Windows (from Vista to Windows 10). Other Linux distributions may work provided Xojo requirements are met. 32-bit SigmoID version runs on 64-bit Linux distributions provided 32-bit libraries are installed; web browser related features require loading 32-bit WebKit 1 libraries (see SigmoID.sh). 64-bit Linux version is compiled with beta version of Xojo compiler and may be less stable. An important limitation of this version is its inability to open standard SigmoID profile (.sig) files (these files are converted to folders on 64-bit Linux; .sig files and folders are fully interchangeable on other platforms). We hope to fix this problem once Xojo compiler is appropriately updated.

Full list of platform-specific system requirements is located at Xojo site: http://developer.xojo.com/system-requirements

Compiled applications for all supported platforms are located on the Releases page.

Additional info and usage instructions are in the help file accessible from SigmoID.

There is also a paper describing SigmoID: Nikolaichik Y, Damienikan AU. (2016) SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals. PeerJ 4:e2056 https://doi.org/10.7717/peerj.2056

As supporting four different systems (and different versions of those) isn't simple, we'd be grateful for reporting any problems via the Issues page.

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