MotifView

MotifView - A motif viewing tool

MotifView at work
Software company	CoGe Team
Analysis Type	Compare multiple genomic regions for motifs
Working state	Testing
Tools Utilized	blastn, LAGAN

MotifView is a tool that visualizes motifs in compared genomic regions.

Introduction

MotifView uses visual and algorithmic tools to visualize motifs within multiple genomic regions. Sharing many functional similarities to GEvo, it's possible to compare sequences from any number of organisms using a variety of different sequence comparison algorithms.

On this page we provide only a brief description of options that are shared with GEvo. If descriptions and directions are ambiguous, please follow the links to specific sections to the GEvo instructions on that section.

There's also the option to use the embedded videos to view demos of the sections following. One can either follow the text along with the video or choose to use either exclusively.

MotifView basics

Screen-shot of where a MotifView analysis is configured. Four genomic regions have been specified by gene name, dataset and the amount of additional upstream/downstream sequence

1. Select genomic regions to analyze
2. Select a sequence alignment algorithm appropriate for the sequences and area of interest
3. Select motifs to visualize
4. Press "Find Motifs!" button

To alternate between these options to configure an analysis, select the appropriate tab.

Sequence Submission

Manual Submission

Select the "Sequence Submission" tab to open these options. Here, you can specify sequence submission boxes for each sequence that will be submitted for a MotifView anlaysis. This is also were you can adjust the amount of sequence analyzed, select which sequences are analyzed, reverse complement a sequence, mask a sequence according the the genomic features it contains, and change the display order of sequences.

The different options for submitting and modifying sequences to be visualized can be found here.

Merging Analyses

Often, there are times when you may want to merge MotifView with previously existing GEvo anlayses. To do this, copy a GEvo link into the text-box next the text: "Merge Previous GEvo Analysis (paste in URL)" located at the top of the sequence submission tab. Then press the "Merge" button". The sequences as specified in the pasted URL will appear as new sequence submission boxes configured as specified in the link (extra up/downstream sequence, reverse complement, masked, etc.)

Alignment Algorithms

While many major algorithms exist for alignment, not all are suitable for the analysis available in MotifView. As such, MotifView compares genes at a scale that makes BlastN and LAGAN the most ideal algorithm choices. The options and suitability of available algorithms is discussed here.

Select Motifs

This tab allows the user to define how and which motifs will be found and analyzed. The "Select Motifs" tab contains four pull down options when choosing motifs for analysis.

Choose TFBS Motif

Users can manually enter a motif in the section "Search for User-Defined Motifs". Also, while colors are automatically provided to motifs, users can define their own color separated from the motif by a colon. For example:

CACGTG:Red

Select from Comprehensive List of Motifs

It's also possible to browse the full list of motifs in our database and add them to be analyzed. In the window presenting the full list, motifs appear by name, then sequence. Information on highlighted motifs will pop up on pressing the "Get Motif Info" button.

Once selected, the motif will appear in the "Selected Motifs" window where they can be additionally deselected or the list cleared entirely for a new list.

Select Motifs from Categories

Additionally, there is a choice of provided motif categories: Stress and Families. Toggling any category will pull a down list of motifs linked to that stress or transcription factor family. If desired, a range of motifs not confined to categories is available below the categories. In addition, users can select or deselect all options in a category if needed.

Once motifs are chosen, press the "Find Motifs!" button above the tabs to begin analysis.

Modifying result graphics

Show preloaded annotations

An important feature when using MotifView is the ability to view other features such as CNSs. In the "Results Parameters" section there is the option to show preloaded annotations in the panel, including CNSs, genespace and PIL5 sites.

Further, one can restrict viewing motifs anywhere except when overlapping with any preloaded annotations. This is especially important because motifs are painted larger in the panel than they would actually appear. Not painting the motifs larger would result in invisible motifs but this representation can appear to make motifs overlap with other features when they do not. Restricting visible motifs to those that overlap with annotations eliminates any such error.

Showing Contigs

Example MotifView result with hsps, genomic feature, CNSs, genespace, and motifs drawn. Note that motifs are also only restricted to viewing those that overlap with genespace or CNSs

Where to find MotifView's options for viewing contigs, HSP labels, and genomic feature labels.

Where to find MotifView's options for viewing contigs, HSP labels, and genomic feature labels.

Some genomes have contig assembly information. To learn how to view this in MotifView's results click here.

Turning on labels for HSPs (blast hits) in MotifView's results

To learn how to draw the HSP number on the HSP click here.

Turning on labels for Genomic Features (e.g. genes) in MotifView's results

If you want to have the feature names drawn on the feature:

1. Select the "Results Parameters" tab from MotifView's configuration box
2. Select "yes" for the option "Label Genomic Features".

• You can have the labels drawn linearly, so each label is at the same vertical position for a track, or staggered, where they are drawn top, middle, bottom alternating.

Expanding Overlapping Features and Regions of Sequence Similarity

Where to find MotifView's options for viewing overlapping genomic features and regions of sequence similarlity.

By default MotifView will drawn overlapping genomic features and regions of sequence similarity on top of one another. However, this sometimes hides some of the interesting complexities in a genomic region such as local duplications or regions containing repeated sequences. To view these, select the "Results Parameters" tab and select "Yes" for "Auto adjust overlapping features" and/or "Auto adjust overlapping HSPs". These options are set to "No" by default because finding and drawing overlapping features can take a long time to process, and are not always useful.

Refining an analysis

Once a MotifView analysis has run, any of the analysis parameters can be changed and re-run after pressing the "Clear all previous analysis" button. Some existing parameters will remain and other will have to be selected again.

The common parameters changed are:

• The extent of the genomic region analyzed. The amount to which the panel extends beyond the gene in question can be changed in the "Left sequence" and "Right sequence" boxes on the "Sequence Submission" tab. Changes to these boxes will remain in new analysis.
• Reverse complementing sequences. This change will remain after previous analysis is cleared.
• Also reset when previous analysis is cleared are the datasets for the sequence submissions, algorithm, and motifs selected. This means that this information will have to defined again after the user clears previous analysis

Hints and Tricks

Sequences with many common sub-sequences

Comparing sequences with lots of common sub-sequences usually causes GEvo to take a very long time processing the analysis (both in terms of identifying the common sequences and generating the final results). Also, if many regions are identified, it is often difficult to make sense of the results. This kind of problem will surface in many large genomes, such as mammal and plant genomes. For example human and maize are both riddled with large amounts of repetitive sequences derived from retroviruses and transposons. This makes the comparison of large genome regions in these genomes difficult, if not impossible. To circumvent this problem, mask all sequence that does not code for protein. You can select this option under the "Sequence options" menu and selecting "non-CDS" for the row "Mask Sequence".

Example Analyses

Analysis of syntenic regions from Arabidopsis thaliana, Carica papaya, and Vitis vinifera

Linking to GEvo

Linking to GEvo is easy! Please see this page on how.

References/Downloads

For a list of all datasets with annotations, click here

For a list of all TFBS motifs used in Spangler et al., New Phytologist (2011) Evidence for Conserved Noncoding Sequence Functions in Arabidopsis thaliana. , click here

For a list of all TFBS motifs used in this site, click here

Bug Report

Progress on bugs can be found here.