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| 4 | <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> |
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| 5 | <title>Help Page for the Laj Applet</title> |
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| 6 | </head> |
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| 7 | <body bgcolor=#FFFFFF> |
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| 8 | <br> |
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| 9 | <p> |
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| 10 | <h2>Help Page for the Laj Applet</h2> |
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| 11 | <br> |
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| 12 | <p> |
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| 13 | TABLE OF CONTENTS |
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| 14 | <ul> |
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| 15 | <li><a href="#intro">Introduction</a> |
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| 16 | <li><a href="#prep">Preparing Your Browser</a> |
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| 17 | <li><a href="#screen">Screen Layout</a> |
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| 18 | <li><a href="#mouse">Mouse Controls</a> |
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| 19 | <li><a href="#menu">Menus and Buttons</a> |
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| 20 | <li><a href="#notes">Footnotes</a> |
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| 21 | </ul> |
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| 22 | <p> |
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| 23 | <br> |
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| 24 | |
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| 25 | <h3><a name="intro">Introduction</a></h3> |
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| 26 | <p> |
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| 27 | Laj is a tool for viewing and manipulating the output from |
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| 28 | pairwise alignment programs such as |
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| 29 | <a href="http://bio.cse.psu.edu/">blastz</a>. It can display |
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| 30 | interactive dotplot, pip, and text representations of the |
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| 31 | alignments, a diagram showing the locations of exons and |
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| 32 | repeats, and annotation links to other web sites containing |
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| 33 | additional information about particular regions. |
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| 34 | <p> |
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| 35 | The program is written in Java in order to provide a |
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| 36 | graphical user interface that is portable across a variety |
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| 37 | of computer platforms; indeed its name stands for "Local |
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| 38 | Alignments with Java". Currently it exists in two forms, |
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| 39 | a stand-alone application and a web-based applet, with |
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| 40 | slightly different capabilities. However, this help page |
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| 41 | will only discuss the applet. |
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| 42 | <p> |
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| 43 | |
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| 44 | <h3><a name="prep">Preparing Your Browser</a></h3> |
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| 45 | <p> |
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| 46 | This applet requires at least Java 1.2, and preferably Java 1.3 |
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| 47 | or higher. For best compatibility, Sun's Java Plug-in |
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| 48 | is recommended. Please see |
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| 49 | <a href="java_plugin_help.html">Installing the Java Plug-in</a> |
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| 50 | for more information. |
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| 51 | <p> |
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| 52 | |
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| 53 | <h3><a name="screen">Screen Layout</a></h3> |
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| 54 | <p> |
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| 55 | The Laj window is divided into several sections. |
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| 56 | Across the top you will see a menu/control bar, and below |
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| 57 | that two indicator lines for displaying information about the |
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| 58 | positions of the mouse pointer and the "mark" |
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| 59 | (<a href="#red">red</a> circle) |
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| 60 | respectively. The controls will be discussed individually |
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| 61 | in the <a href="#menu">Menus and Buttons</a> section of this |
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| 62 | document. |
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| 63 | <p> |
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| 64 | <i>Ruler:</i><br> |
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| 65 | The first graphical panel is a horizontal ruler that displays |
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| 66 | tick marks corresponding to positions in the first aligned |
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| 67 | sequence. These are intended to give you an immediate |
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| 68 | general feel for the location and scale of the region being |
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| 69 | displayed. Precise locations can be determined via the |
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| 70 | position indicator, which displays the exact coordinate of |
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| 71 | the mouse pointer. |
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| 72 | <p> |
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| 73 | <i>Dotplot:</i><br> |
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| 74 | The large middle panel displays a dotplot view of the |
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| 75 | alignments, with the first sequence (often human) along |
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| 76 | the horizontal <tt>x</tt>-axis and the second sequence |
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| 77 | (e.g., mouse) along the vertical <tt>y</tt>-axis. If the |
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| 78 | second sequence contains multiple contigs, they will appear |
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| 79 | as separate horizontal bands across the plot, each with its |
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| 80 | own <tt>y</tt>-axis coordinate system. Whenever |
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| 81 | the mouse pointer is in this panel, the position indicator |
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| 82 | displays its location in the format "<tt>x,y</tt>", where |
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| 83 | <tt>x</tt> is the position in the horizontal sequence and |
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| 84 | <tt>y</tt> is the position in the vertical sequence. If |
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| 85 | there are multiple contigs, then the first word of the |
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| 86 | contig name will be displayed as well. |
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| 87 | <p> |
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| 88 | <i>Annotation links:</i><br> |
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| 89 | Below the dotplot is a panel that provides links to |
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| 90 | additional information about various sequence regions. Each |
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| 91 | annotation is represented by a color-coded bar spanning the |
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| 92 | region's position in the first sequence. The bars' |
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| 93 | vertical positions are not meaningful; they are placed in |
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| 94 | rows only for convenience, to keep them from overlapping. |
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| 95 | Pointing to a particular bar will cause the position |
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| 96 | indicator to display the <tt>x</tt> coordinate of the |
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| 97 | pointer, and also the type and description of that bar's |
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| 98 | annotation; otherwise only the <tt>x</tt> coordinate will be |
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| 99 | shown. Clicking on a bar will open a separate browser |
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| 100 | window to visit the corresponding web site. If no annotation |
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| 101 | file was provided, this panel will not appear. |
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| 102 | <p> |
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| 103 | <i>Sequence features:</i><br> |
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| 104 | The next panel contains a schematic diagram of the |
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| 105 | known exons, repeats, and other features in the first |
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| 106 | sequence, if these files were provided. Again, the position |
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| 107 | indicator displays the <tt>x</tt> coordinate of the mouse |
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| 108 | pointer, and also identifies any features at that position. |
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| 109 | <p> |
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| 110 | <i>Pip:</i><br> |
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| 111 | The next panel displays a pip (percent identity plot) view |
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| 112 | of the alignments. This is similar to the dotplot, |
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| 113 | except that the vertical scale represents the percentage of |
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| 114 | matching nucleotides in each gap-free segment of a local |
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| 115 | alignment, instead of its position in the second sequence. |
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| 116 | Only the top half of the plot is shown, since segments |
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| 117 | matching less than 50% are not very interesting. An |
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| 118 | additional feature of this panel is that colored backgrounds, |
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| 119 | or "underlays", may be used to highlight regions of interest. |
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| 120 | The position indicator displays the horizontal coordinate |
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| 121 | and vertical percentage position of the mouse pointer, and |
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| 122 | it can also display labels for the colored regions if these |
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| 123 | were provided. |
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| 124 | <p> |
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| 125 | <i>Text view:</i><br> |
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| 126 | The bottom panel displays a nucleotide-level view of a single |
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| 127 | selected local alignment. (Initially it is blank, since you |
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| 128 | haven't selected anything yet.) The top row of this display |
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| 129 | shows the nucleotide sequence from the first species |
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| 130 | (<tt>x</tt>-axis in the dotplot), while the bottom row shows |
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| 131 | the sequence from the second one (<tt>y</tt>-axis). Both |
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| 132 | sequences will likely have had gaps inserted by the alignment |
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| 133 | program. The middle row contains symbols to |
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| 134 | indicate how well the nucleotides match at each position; |
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| 135 | this matching is case-insensitive to deal with soft masking, |
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| 136 | but non-nucleotide characters such as <tt>X</tt> or <tt>N</tt> |
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| 137 | never match anything, even themselves. |
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| 138 | Note that most |
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| 139 | of the local alignments will be much too long to fit across |
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| 140 | this window, so a scrollbar is provided; the |
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| 141 | relative size of the scrollbar's slider indicates what fraction |
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| 142 | of the alignment is shown in the window. Shaded "highlights" |
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| 143 | similar to the pip underlays may also appear. Whenever |
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| 144 | the mouse pointer is in this bottom panel, the position |
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| 145 | indicator displays its location in the |
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| 146 | format "<tt>n:x,y</tt>", where <tt>n</tt> is the column position |
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| 147 | in the text representation of the alignment (starting with 0), |
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| 148 | while <tt>x</tt> and <tt>y</tt> are the sequence positions |
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| 149 | in the top and bottom rows, respectively (starting with 1). |
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| 150 | Note that <tt>x</tt> and <tt>y</tt> do not include the gaps, |
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| 151 | but <tt>n</tt> does. Labels for any highlights at that |
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| 152 | position are also displayed. |
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| 153 | <p> |
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| 154 | With the exception of the text view, all of these panels |
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| 155 | use the same horizontal coordinate scale (i.e., position in |
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| 156 | the first sequence), and they are always kept vertically |
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| 157 | aligned so they can be compared easily. |
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| 158 | <p> |
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| 159 | |
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| 160 | <h3><a name="mouse">Mouse Controls</a></h3> |
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| 161 | <p> |
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| 162 | You can select a particular local alignment in the dotplot |
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| 163 | or pip by clicking on one of its segments with the left mouse |
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| 164 | button. (Actually you don't have to click exactly on it, |
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| 165 | because Laj will automatically jump to the nearest point in |
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| 166 | the same contig if you miss.) The spot will be marked with a |
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| 167 | small <a href="#red">red</a> circle |
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| 168 | in both the dotplot and the pip, and the entire local |
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| 169 | alignment containing the mark will change color from black |
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| 170 | to <a href="#red">red</a> |
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| 171 | (each local alignment typically spans several |
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| 172 | gap-free "segments"). Also, the corresponding text view for |
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| 173 | that alignment will appear in the bottom panel with the |
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| 174 | selected position highlighted. This requires loading the |
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| 175 | sequence files, so it may take a few moments. Lastly, the |
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| 176 | mark indicator line will be filled in with information about |
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| 177 | the marked alignment and position, including the contig name |
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| 178 | if the second sequence is fragmented. Note that there is only |
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| 179 | one mark at a time, so the previous one, if any, will be |
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| 180 | unmarked. |
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| 181 | <p> |
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| 182 | In a similar fashion, clicking the left mouse button in the |
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| 183 | text view will move the mark (both the highlight and the |
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| 184 | <a href="#red">red</a> circle) to that position |
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| 185 | (though sometimes you have to click twice). |
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| 186 | However, gap positions cannot be selected in this manner |
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| 187 | because they do not correspond to pip segments; if |
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| 188 | you click in a gap, the left end of the gap is selected |
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| 189 | instead. |
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| 190 | <p> |
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| 191 | As mentioned earlier, clicking on an annotation bar will |
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| 192 | open a separate browser window to visit the corresponding |
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| 193 | web site, but clicking in the ruler or feature panel has no |
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| 194 | effect. |
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| 195 | <p> |
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| 196 | You can "zoom in" on a particular region by dragging out a |
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| 197 | rectangle with the left mouse button in any of the white |
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| 198 | panels (ruler, dotplot, annotations, features, or pip). All |
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| 199 | of these panels will always zoom together, to keep them lined |
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| 200 | up. This can be repeated until the maximum resolution is |
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| 201 | reached; after that Laj will display an error message. |
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| 202 | Note that selecting your zoom in a non-dotplot panel only |
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| 203 | zooms horizontally (the zoom rectangle is always |
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| 204 | full-height), so to keep the dotplot looking nice it is best |
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| 205 | to select your zoom there, and keep the zoom rectangle |
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| 206 | roughly proportional to the dimensions of the existing |
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| 207 | dotplot panel. |
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| 208 | <p> |
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| 209 | Holding down the right mouse button over any of the white |
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| 210 | panels adds crosshairs at the mouse pointer's location, which |
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| 211 | is convenient for determining whether two regions really line |
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| 212 | up. If you have a one-button mouse, you can achieve the same |
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| 213 | effect by applying the <code>Shift</code> key when initially |
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| 214 | pressing the mouse button. |
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| 215 | <p> |
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| 216 | |
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| 217 | <h3><a name="menu">Menus and Buttons</a></h3> |
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| 218 | <p> |
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| 219 | <dl> |
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| 220 | <dt>File - Save: |
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| 221 | <dd> |
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| 222 | Allows you to save the alignments that you have flagged (see below) |
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| 223 | by sending them back to the server in a format similar to the input. |
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| 224 | What the server does with them depends on the site. For example, |
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| 225 | if you are running Laj via <a href="http://www.bx.psu.edu/">Galaxy</a>, |
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| 226 | they will be stored as a new dataset in your history for further |
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| 227 | analysis. A different site might email the file to you, reflect |
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| 228 | it to your browser, or use it in some other way. If the site does |
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| 229 | not specify a URL for sending the alignments, this menu item will not |
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| 230 | appear. |
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| 231 | <p> |
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| 232 | <dt>File - Exit: |
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| 233 | <dd> |
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| 234 | Closes the Laj window. |
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| 235 | <p> |
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| 236 | <dt>Tools - Flag: |
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| 237 | <dd> |
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| 238 | Flags the currently selected local alignment (the one containing the |
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| 239 | <a href="#red">red</a> mark circle) by changing its color. You can |
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| 240 | repeat this on other alignments to build a flagged set. The flagged |
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| 241 | alignments are normally green, but if one is also the currently |
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| 242 | selected alignment (e.g. when you have just flagged it), it can't be |
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| 243 | both green and red so it is orange instead. Also, just like the |
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| 244 | <a href="#red">red</a> circle, all of these colors will be displayed |
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| 245 | differently against colored backgrounds. |
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| 246 | <p> |
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| 247 | <dt>Tools - Unflag: |
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| 248 | <dd> |
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| 249 | Changes the local alignment containing the <a href="#red">red</a> |
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| 250 | circle back to its original color. |
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| 251 | <p> |
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| 252 | <dt>Tools - Unzoom: |
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| 253 | <dd> |
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| 254 | Restores all of the white panels back to the original, unzoomed view. |
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| 255 | <p> |
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| 256 | <dt>Help - About: |
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| 257 | <dd> |
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| 258 | Displays a message window with information about Laj, including |
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| 259 | version, author, etc. |
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| 260 | <p> |
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| 261 | <dt>Help - Manual: |
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| 262 | <dd> |
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| 263 | Displays this help page in a separate browser window. |
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| 264 | <p> |
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| 265 | <dt>Help - Keys: |
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| 266 | <dd> |
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| 267 | Displays a message window listing Laj's keyboard shortcuts. No |
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| 268 | <i>Alt</i> key is needed, since Laj doesn't use the keyboard for |
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| 269 | much else. |
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| 270 | </dl> |
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| 271 | <p> |
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| 272 | |
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| 273 | <!-- <hr align=left noshade size=1 width="20%" color=black> --> |
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| 274 | <h3><a name="notes">Footnotes</a></h3> |
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| 275 | <p> |
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| 276 | <a name="red"></a> |
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| 277 | [1] |
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| 278 | The circular mark and its local alignment are red |
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| 279 | when the background is white, but are displayed in different |
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| 280 | colors against other backgrounds to ensure good contrast. |
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| 281 | <p> |
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| 282 | |
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| 283 | <br> |
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| 284 | <p> |
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| 285 | <hr> |
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| 286 | <i>Cathy Riemer, August 2006</i> |
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| 287 | |
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| 288 | <!-- These blank lines allow the browser to scroll properly |
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| 289 | to the last anchor target. --> |
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