SequenceJuxtaposer Readme

James Slack
Kristian Hildebrand
Tamara Munzner
University of British Columbia
{jslack,hilde,tmm}@cs.ubc.ca

Katerine St. John
City University of New York
stjohn@lehman.cuny.edu

January 11, 2004

http://www.cs.ubc.ca/labs/imager/imager-web/Research/2003/SequenceJuxtaposer/

1 	What is SequenceJuxtaposer?
2 	Loading FASTA files
3 	Searching for motifs
3.1 	  Keyboard input
3.2 	  Mouse input
3.3 	  Mouse navigating
3.3.1 	    Bounding box resizing
3.3.2 	    Site resizing
4 	Resizing an area of interest
5 	Changing colors of groups and sites
6 	Differences


1 What is SequenceJuxtaposer?

Sequence Juxtaposer is a flexible tool used to explore a set of sequences.  It
provides an immediate view of a set of sequences that a user can navigate
through with a few clicks of a mouse.


2 Loading FASTA files

A FASTA file (DNA, RNA, or other protein sequence) can be loaded into
  SequenceJuxtaposer as long as it is aligned.  That is, all sequences that
  are loaded must have identical length; gaps may be inserted as well to
  provide alignment.  A FASTA file is either passed into SequenceJuxtaposer
  as a command-line argument as follows:

	java -jar sj.jar fastaFile.fa

  or SequenceJuxtaposer can be started and a file can be loaded using the
  graphical interface:

	java -jar sj.jar


3 Searching for motifs

You may search for a motif in a few ways: Keyboard input, Mouse input, and
  Mouse navigating.

3.1 Keyboard input

If the motif you are searching for is very short (i.e. start codon) it may
  by typed into the search box at the bottom of the display screen.  Pressing
  enter after typing your search (or clicking the search button) will perform
  a search in the data.  All locations of your input motif will be highlighted
  with a magenta box if there aren't too many results (i.e. searching for
  a single base pair character may not be displayed in very large data sets).
  Please see the section of this document entitled "Resizing the found group"
  for another useful tool related to the search motif.


3.2 Mouse input

If you know the position of a motif in a loaded sequence, select the motif
  using a mouse by clicking at the start of the motif and dragging to the end,
  releasing the mouse when you are at the other end of the motif.  This action
  copies the motif to the search box and highlights the other locations of
  the selected motif in the loaded sequences.  The text in the search box can
  now be modified and a new search can be performed with small changes.
  A motif that is too long to fully display will be truncated; you may edit 
  a small range of base pairs at the start and/or end of a large motif.


3.3 Mouse navigating

Motif searching can also be achieved without using the previously mentioned
  searching techniques; simple navigation is possible if you know where you
  would like to explore spatially.  There are two possible methods for 
  interactive resizing: bounding box resizing and base pair site resizing.

3.3.1 Bounding box resizing

By pressing the Control (Ctrl) key and dragging a box around a subset of
  base pair sites and a subset of sequences, not releasing the Ctrl key but
  releasing the mouse, and using the mouse to drag the box larger, you may
  stretch the region in the box to any size you want.  This also resizes the
  areas outside the box accordingly.  Navigation with the mouse in this
  manner is a very powerful tool for "growing" or "shrinking" a selection
  of base pair sites across sequences.

3.3.2 Site resizing

By pressing the Shift key and dragging the mouse, a single site may be 
  stretched larger.  This action also resizes the rest of the view 
  (sequences and sites) accordingly.  Navaigation with the mouse with this 
  feature is similar to the previous Bounding box resizing method with a 
  single base pair site, but doesn't require a bounding box to be defined.


4 Resizing an area of interest

Using the "Groups" panel, you can resize different groups.  The resizing can
  either make the selected group "smaller" by shrinking each member
  horizontally or "bigger" by growing each member horizontally.  The groups
  that can be resized this way are indicated by radio buttons in the
  "Groups" panel.  They include: gaps, search results, and differences.


5 Changing colors of groups and sites

The color of a group (base pair sites, gaps, differences, searched for results)
  can be changed through the "Groups" panel by clicking on the color swatch.


6 Differences

Differences in aligned sequences are computed at run-time.  They may be turned
  off in the "Groups" panel.  This group is intended to be a guide in sets
  of very similar sequences as even the smallest differences can be found
  in large data sets due to SequenceJuxtaposer's guarantee of groups always
  being visible.