MotifView2

-- Krdeleon 16:04, 30 August 2011 (UTC)

MotifView - A motif viewing tool

MotifView at work
Software company	CoGe Team
Analysis Type	Compare multiple genomic regions for motifs
Working state	Released
Tools Utilized	blastn, tblastx, blastz, CHAOS, LAGAN, DiAlign 2
Website	http://synteny.cnr.berkeley.edu/CoGe/MotifView.pl

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.

MotifView basics

Screen-shot of where a MotifView analysis is configured. Two genomic regions have been specified by gene name 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 questions in mind
3. Select motifs to visualize and how to visualize them
4. Press "Find Motifs!" button

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

Sequence 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.

Alignment Algorithms

While the default alignment algorithm will be useful for most queries, we've provided many major algorithms for use in alignment. 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.

Select Graphic Type

Determine if you'd like to see the motifs represented visually as a diamond or flag

Show Motifs overlapping with CNSs or any position in the Window

Motifs are often found within CNSs as protein binding sites or other functional DNA. However, motifs appear in many places and can be viewed anywhere in the window.

Choose TFBS Motif

You can manually enter a motif in the window next to "Enter TFBS Motif Regular Expression :".

Additionally, there is a choice of provided motif categories. On toggling any category a pull down list of motifs linked to that stress, transcription factor family, etc, will appear for selection. If desired, a range of motifs not confined to categories is available below the categories.

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

Regenerating/Saving a MotifView Analysis

MotifView has the ability to regenerate past comparisons or save current comparisons. The ability to create links to, view, or save MotifView analyses is described in detail here.

Modifying result graphics

Showing Contigs

Example MotifView result with contigs, hsp labels, and genomic feature labels drawn.

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

Some genomes have contig assembly information. To view this in MotifView's results:

1. Select the "Results Parameters" tab from MotifView's configuration box
2. Select "yes" for the option "Color contigs red".

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

If you want to have the HSP number drawn on the HSP:

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

• 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.

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.

Example of MotifView result with local duplications that are obfuscated by not showing separating overlapping HSPs. Comparison is between orthologous regions of Arabidopsis thaliana and Arabidopsis lyrata. (A) No wedges drawn connecting regions of sequence similarity. (B) Wedges drawn connecting regions of sequence similarity. Note the "messy" regions where the local duplication is. Results can be regenerated at http://tinyurl.com/mokdnn .

vo results with "auto adjust" HSP and Genomic Features turned on. This causes MotifView to find genomic features and blast-hits that overlap at the same position, and drawn them such that they are separated in order to identify local duplications in a genomic region, repeat sequences, and alternatively spliced transcripts. This is a comparison between orthologous regions of Arabidopsis thaliana and Arabidopsis lyrata, and can be regenerated at http://tinyurl.com/mokdnn. Wedges have been drawn connection regions of sequence similarity between one gene in the bottom panel. This shows that this one gene has sequence similar to four regions in the orthologous genomic region, which is indicative of a local gene duplication. Also, there is a "stack" of HSPs which is caused by repeated sequences. Note that two genes have annotations for being alternatively spliced, which is visualized by separating the drawing of overlapping genomic features.

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.

Merging Analyses

Often, there are times when you will want to merge together two or more separate 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.)

Refining an analysis

Once a GEvo analysis has run, you can change any of the analysis parameters and re-run the analysis by pressing the "Run GEvo analysis" button again. The common parameters changed are:

• The extent of the genomic region analyzed. The interactive results make this easy with slider bars.
• The algorithm used in the analysis
• Masking sequences
• Skipping sequences
• Reverse complementing sequences
• The coloration and information displayed in the result's graphics

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.