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This repository contains two pieces of software: a programming library for reading and writing XMS formatted motif set files for a number of popular programming languages used for bioinformatics projects, and iMotifs, which is a sequence motif editor and analysis environment built with Objective-C and Java for Mac OS X.
iMotifs is a powerful yet easy to use sequence motif viewer and editor for the Apple Mac computers (Leopard or later). iMotifs is a research tool for computational biologists that allows viewing, editing and analysing XMS formatted sequence motif set files (position weight matrices).
Read the Getting Started with iMotifs guide for basic usage instructions.
Matias Piipari , Thomas A. Down , Harpreet Saini , Anton Enright , and Tim J.P. Hubbard iMotifs: an integrated sequence motif visualization and analysis environment Bioinformatics Advance Access published on January 26, 2010, DOI 10.1093/bioinformatics/btq026.
Installation: double-click the downloaded DMG package in Finder and drag to Applications.
We provide an API for reading and writing XMS formatted motif data with Perl, Ruby, R and Objective-C languages.
Each of the libraries includes basic installation instructions, information about dependencies and a usage example and all are licensed under the LGPL 2.0.
Java support for reading and writing XMS formatted sequence motif files is available as part of BioJava.
- View sequence logos for motifs
- View motif hits in a set of sequences
- Annotate motifs with freeform metadata (e.g. notes, TRANSFAC accessions, etc)
- Rename motifs easily either individually or in batch (add prefixes, suffixes)
- Add pseudocounts to motifs
- Reverse complement motifs
- PDF output
- TRANSFAC formatted motif file import and export support
- Printing support
- Search by motif name or consensus sequence
- QuickLook plugin for viewing motif files with Finder and other QuickLook supporting applications (e.g. the Cyberduck SFTP client)
- Drag & Drop motifs between motif sets in iMotifs, or to Finder
- Find closest matching or reciprocally matching motif pairs between motif sets (distance metric from Down et al, 2007)
- Present motif multiple alignments: you can move motifs, or load files containing offsets.
- Calculate motif multiple alignments
- Drag in sequence FASTA files to discover sequence motifs with NestedMICA
- Retrieve promoter / 3’ UTR sequence from Ensembl using annotations (allows for keyword searching)
- Retrieve sequence features (GFF) and ChIP-seq peak sequences (SWEMBL/MACS/FindPeaks) from Ensembl
- Assign motif significance score threshold
- Calculate motif overrepresentation in a positive versus a negative sequence set (ROC-AUC value)
- Scan sequences with motifs
- It’s multithreaded: you can keep working on motifs whilst multiple alignments or motif-motif matches are being computed.
iMotifs includes an integrated NestedMICA (Down et al, 2005) motif inference suite as well as a previously unpublished motif analysis package nmica-extra.
Installation: double-click the downloaded DMG package in Finder and drag to Applications.
This development build is regularly and automatically updated (using Sparkle). You can read more about changes between versions it in the release notes.
Installing the QuickLook plugin (optional)
- Drag the plugin from the installation package to /Library/QuickLook or to ~/Library/QuickLook (you might have to create the QuickLook directory under your home directory if it’s not there already)
- Restart Finder (or log out and back in)
Please report issues you experience to the iMotifs mailing list. Click "Join this group" on the group page to join.
Below you’ll find some screencast videos and screenshots of iMotifs. For more screenshots, see the Downloads page and the Getting Started guide.
Searching and aligning GATA motifs
Editing motif annotations
Motif set thumbnails and QuickLook previewing
See Getting Started for a beginner’s guide to using iMotifs.
iMotifs is licensed under the GNU Lesser General Public License Version 3.
- NestedMICA (Down et al, 2005) motif inference. Note that the NestedMICA build currently included with iMotifs is Matias Piipari’s development branch.
- a previously unpublished crossplatform (Java based) motif analysis package nmica-extra (includes motif alignment, sequence retrieval etc).
We’d also like to warmly thank the authors of the following libraries that are linked to and packaged with iMotifs:
- BioCocoa: sequence file parsing
- ActiveRecord: SQL database connectivity
- BWToolkit: transparent panels and UI widgets.
- Updates are served with Choctop and Sparkle
Is your favourite feature missing? Your contributions to iMotifs are of course welcome! Here’s instructions for getting iMotifs to compile to help you get started:
The project has been moved over to GitHub and there are no dependencies between different Xcode projects anymore. After installing the developer tools and cloning the iMotifs project repository you need to get a check out of the NestedMICA and nmica-extra packages, and download the external dependencies Sparkle and BWToolkit. Now you’re ready to build the iMotifs project. In more detail:
- Install Xcode. You’ll need OS X 10.5 and Xcode 3.1 (or later).
- Open up the Terminal app
- Check out iMotifs:
git clone http://www.github.com/mz2/imotifs
- Check out Matias Piipari’s NestedMICA development branch:
svn checkout http://www.derkholm.net/svn/repos/nmica/branches/mp4-13112008/ nmica-dev
- Check out the nmica-extra motif analysis package:
svn checkout http://www.derkholm.net/svn/repos/nmica-extra/
- Follow the the Sparkle framework installation instructions.
- Install the BWToolkit framework installation instructions.
- Open iMotifs in Xcode:
open imotifs/iMotifs.xcodeproj
- Press the Build button.
If you have problems getting iMotifs to compile or run, or you want to post a patch, please email the iMotifs mailing list.