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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
2<html>
3<head>
4<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
5<title>Help Page for the Laj Applet</title>
6</head>
7<body bgcolor=#FFFFFF>
8<br>
9<p>
10<h2>Help Page for the Laj Applet</h2>
11<br>
12<p>
13TABLE OF CONTENTS
14<ul>
15<li><a href="#intro">Introduction</a>
16<li><a href="#prep">Preparing Your Browser</a>
17<li><a href="#screen">Screen Layout</a>
18<li><a href="#mouse">Mouse Controls</a>
19<li><a href="#menu">Menus and Buttons</a>
20<li><a href="#notes">Footnotes</a>
21</ul>
22<p>
23<br>
24
25<h3><a name="intro">Introduction</a></h3>
26<p>
27Laj is a tool for viewing and manipulating the output from
28pairwise alignment programs such as
29<a href="http://bio.cse.psu.edu/">blastz</a>.  It can display
30interactive dotplot, pip, and text representations of the
31alignments, a diagram showing the locations of exons and
32repeats, and annotation links to other web sites containing
33additional information about particular regions.
34<p>
35The program is written in Java in order to provide a
36graphical user interface that is portable across a variety
37of computer platforms; indeed its name stands for "Local
38Alignments with Java".  Currently it exists in two forms,
39a stand-alone application and a web-based applet, with
40slightly different capabilities.  However, this help page
41will only discuss the applet.
42<p>
43
44<h3><a name="prep">Preparing Your Browser</a></h3>
45<p>
46This applet requires at least Java 1.2, and preferably Java 1.3
47or higher.  For best compatibility, Sun's Java Plug-in
48is recommended.  Please see
49<a href="java_plugin_help.html">Installing the Java Plug-in</a>
50for more information.
51<p>
52
53<h3><a name="screen">Screen Layout</a></h3>
54<p>
55The Laj window is divided into several sections.
56Across the top you will see a menu/control bar, and below
57that two indicator lines for displaying information about the
58positions of the mouse pointer and the "mark"
59(<a href="#red">red</a> circle)
60respectively.  The controls will be discussed individually
61in the <a href="#menu">Menus and Buttons</a> section of this
62document.
63<p>
64<i>Ruler:</i><br>
65The first graphical panel is a horizontal ruler that displays
66tick marks corresponding to positions in the first aligned
67sequence.  These are intended to give you an immediate
68general feel for the location and scale of the region being
69displayed.  Precise locations can be determined via the
70position indicator, which displays the exact coordinate of
71the mouse pointer.
72<p>
73<i>Dotplot:</i><br>
74The large middle panel displays a dotplot view of the
75alignments, with the first sequence (often human) along
76the horizontal <tt>x</tt>-axis and the second sequence
77(e.g., mouse) along the vertical <tt>y</tt>-axis.  If the
78second sequence contains multiple contigs, they will appear
79as separate horizontal bands across the plot, each with its
80own <tt>y</tt>-axis coordinate system.  Whenever
81the mouse pointer is in this panel, the position indicator
82displays its location in the format "<tt>x,y</tt>", where
83<tt>x</tt> is the position in the horizontal sequence and
84<tt>y</tt> is the position in the vertical sequence.  If
85there are multiple contigs, then the first word of the
86contig name will be displayed as well.
87<p>
88<i>Annotation links:</i><br>
89Below the dotplot is a panel that provides links to
90additional information about various sequence regions.  Each
91annotation is represented by a color-coded bar spanning the
92region's position in the first sequence.  The bars'
93vertical positions are not meaningful; they are placed in
94rows only for convenience, to keep them from overlapping.
95Pointing to a particular bar will cause the position
96indicator to display the <tt>x</tt> coordinate of the
97pointer, and also the type and description of that bar's
98annotation; otherwise only the <tt>x</tt> coordinate will be
99shown.  Clicking on a bar will open a separate browser
100window to visit the corresponding web site.  If no annotation
101file was provided, this panel will not appear.
102<p>
103<i>Sequence features:</i><br>
104The next panel contains a schematic diagram of the
105known exons, repeats, and other features in the first
106sequence, if these files were provided.  Again, the position
107indicator displays the <tt>x</tt> coordinate of the mouse
108pointer, and also identifies any features at that position.
109<p>
110<i>Pip:</i><br>
111The next panel displays a pip (percent identity plot) view
112of the alignments.  This is similar to the dotplot,
113except that the vertical scale represents the percentage of
114matching nucleotides in each gap-free segment of a local
115alignment, instead of its position in the second sequence.
116Only the top half of the plot is shown, since segments
117matching less than 50% are not very interesting.  An
118additional feature of this panel is that colored backgrounds,
119or "underlays", may be used to highlight regions of interest.
120The position indicator displays the horizontal coordinate
121and vertical percentage position of the mouse pointer, and
122it can also display labels for the colored regions if these
123were provided.
124<p>
125<i>Text view:</i><br>
126The bottom panel displays a nucleotide-level view of a single
127selected local alignment.  (Initially it is blank, since you
128haven't selected anything yet.)  The top row of this display
129shows the nucleotide sequence from the first species
130(<tt>x</tt>-axis in the dotplot), while the bottom row shows
131the sequence from the second one (<tt>y</tt>-axis).  Both
132sequences will likely have had gaps inserted by the alignment
133program.  The middle row contains symbols to
134indicate how well the nucleotides match at each position;
135this matching is case-insensitive to deal with soft masking,
136but non-nucleotide characters such as <tt>X</tt> or <tt>N</tt>
137never match anything, even themselves.
138Note that most
139of the local alignments will be much too long to fit across
140this window, so a scrollbar is provided; the
141relative size of the scrollbar's slider indicates what fraction
142of the alignment is shown in the window.  Shaded "highlights"
143similar to the pip underlays may also appear.  Whenever
144the mouse pointer is in this bottom panel, the position
145indicator displays its location in the
146format "<tt>n:x,y</tt>", where <tt>n</tt> is the column position
147in the text representation of the alignment (starting with 0),
148while <tt>x</tt> and <tt>y</tt> are the sequence positions
149in the top and bottom rows, respectively (starting with 1).
150Note that <tt>x</tt> and <tt>y</tt> do not include the gaps,
151but <tt>n</tt> does.  Labels for any highlights at that
152position are also displayed.
153<p>
154With the exception of the text view, all of these panels
155use the same horizontal coordinate scale (i.e., position in
156the first sequence), and they are always kept vertically
157aligned so they can be compared easily.
158<p>
159
160<h3><a name="mouse">Mouse Controls</a></h3>
161<p>
162You can select a particular local alignment in the dotplot
163or pip by clicking on one of its segments with the left mouse
164button.  (Actually you don't have to click exactly on it,
165because Laj will automatically jump to the nearest point in
166the same contig if you miss.)  The spot will be marked with a
167small <a href="#red">red</a> circle
168in both the dotplot and the pip, and the entire local
169alignment containing the mark will change color from black
170to <a href="#red">red</a>
171(each local alignment typically spans several
172gap-free "segments").  Also, the corresponding text view for
173that alignment will appear in the bottom panel with the
174selected position highlighted.  This requires loading the
175sequence files, so it may take a few moments.  Lastly, the
176mark indicator line will be filled in with information about
177the marked alignment and position, including the contig name
178if the second sequence is fragmented.  Note that there is only
179one mark at a time, so the previous one, if any, will be
180unmarked.
181<p>
182In a similar fashion, clicking the left mouse button in the
183text view will move the mark (both the highlight and the
184<a href="#red">red</a> circle) to that position
185(though sometimes you have to click twice).
186However, gap positions cannot be selected in this manner
187because they do not correspond to pip segments; if
188you click in a gap, the left end of the gap is selected
189instead.
190<p>
191As mentioned earlier, clicking on an annotation bar will
192open a separate browser window to visit the corresponding
193web site, but clicking in the ruler or feature panel has no
194effect.
195<p>
196You can "zoom in" on a particular region by dragging out a
197rectangle with the left mouse button in any of the white
198panels (ruler, dotplot, annotations, features, or pip).  All
199of these panels will always zoom together, to keep them lined
200up.  This can be repeated until the maximum resolution is
201reached; after that Laj will display an error message.
202Note that selecting your zoom in a non-dotplot panel only
203zooms horizontally (the zoom rectangle is always
204full-height), so to keep the dotplot looking nice it is best
205to select your zoom there, and keep the zoom rectangle
206roughly proportional to the dimensions of the existing
207dotplot panel.
208<p>
209Holding down the right mouse button over any of the white
210panels adds crosshairs at the mouse pointer's location, which
211is convenient for determining whether two regions really line
212up.  If you have a one-button mouse, you can achieve the same
213effect by applying the <code>Shift</code> key when initially
214pressing the mouse button.
215<p>
216
217<h3><a name="menu">Menus and Buttons</a></h3>
218<p>
219<dl>
220<dt>File - Save:
221<dd>
222Allows you to save the alignments that you have flagged (see below)
223by sending them back to the server in a format similar to the input.
224What the server does with them depends on the site.  For example,
225if you are running Laj via <a href="http://www.bx.psu.edu/">Galaxy</a>,
226they will be stored as a new dataset in your history for further
227analysis.  A different site might email the file to you, reflect
228it to your browser, or use it in some other way.  If the site does
229not specify a URL for sending the alignments, this menu item will not
230appear.
231<p>
232<dt>File - Exit:
233<dd>
234Closes the Laj window.
235<p>
236<dt>Tools - Flag:
237<dd>
238Flags the currently selected local alignment (the one containing the
239<a href="#red">red</a> mark circle) by changing its color.  You can
240repeat this on other alignments to build a flagged set.  The flagged
241alignments are normally green, but if one is also the currently
242selected alignment (e.g. when you have just flagged it), it can't be
243both green and red so it is orange instead.  Also, just like the
244<a href="#red">red</a> circle, all of these colors will be displayed
245differently against colored backgrounds. 
246<p>
247<dt>Tools - Unflag:
248<dd>
249Changes the local alignment containing the <a href="#red">red</a>
250circle back to its original color.
251<p>
252<dt>Tools - Unzoom:
253<dd>
254Restores all of the white panels back to the original, unzoomed view.
255<p>
256<dt>Help - About:
257<dd>
258Displays a message window with information about Laj, including
259version, author, etc.
260<p>
261<dt>Help - Manual:
262<dd>
263Displays this help page in a separate browser window.
264<p>
265<dt>Help - Keys:
266<dd>
267Displays a message window listing Laj's keyboard shortcuts.  No
268<i>Alt</i> key is needed, since Laj doesn't use the keyboard for
269much else.
270</dl>
271<p>
272
273<!-- <hr align=left noshade size=1 width="20%" color=black> -->
274<h3><a name="notes">Footnotes</a></h3>
275<p>
276<a name="red"></a>
277[1]&nbsp;
278The circular mark and its local alignment are red
279when the background is white, but are displayed in different
280colors against other backgrounds to ensure good contrast.
281<p>
282
283<br>
284<p>
285<hr>
286<i>Cathy Riemer, August 2006</i>
287
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330</body>
331</html>
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