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Manual: Motif/Annotation documentation
author
Brandon King
<kingb@caltech.edu>
Thu, 18 May 2006 23:51:55 +0000
(23:51 +0000)
committer
Brandon King
<kingb@caltech.edu>
Thu, 18 May 2006 23:51:55 +0000
(23:51 +0000)
doc/manual/mussagl_manual.rst
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diff --git
a/doc/manual/mussagl_manual.rst
b/doc/manual/mussagl_manual.rst
index ebf16d36a4be94c6beb344f215dca9e2d2d4c754..615160444f2e896929ec0aba52bdedd692dc7086 100644
(file)
--- a/
doc/manual/mussagl_manual.rst
+++ b/
doc/manual/mussagl_manual.rst
@@
-62,7
+62,8
@@
Supported Platforms:
Download
--------
Download
--------
-Mussagl can be downloaded from http://mussa.caltech.edu/.
+Mussagl in binary form for OS X and Windows and/or source can be
+downloaded from http://mussa.caltech.edu/.
Install
-------
Install
-------
@@
-157,7
+158,9
@@
Instructions:
Now click on the 'Browse' button next to the sequence input box and
then select /examples/seq/human_mck_pro.fa file. Do the same in the
next two sequence input boxes selecting mouse_mck_pro.fa and
Now click on the 'Browse' button next to the sequence input box and
then select /examples/seq/human_mck_pro.fa file. Do the same in the
next two sequence input boxes selecting mouse_mck_pro.fa and
-rabbit_mck_pro.fa as shown below.
+rabbit_mck_pro.fa as shown below. Note that you can create annotation
+files using the mussa `Annotation File Format` to add annotations to
+your sequence.
.. image:: images/define_analysis_step2.png
:alt: Choose sequences
.. image:: images/define_analysis_step2.png
:alt: Choose sequences
@@
-384,15
+387,40
@@
Annotations / Motifs
Annotations
~~~~~~~~~~~
Annotations
~~~~~~~~~~~
+Currently annotations can be added to a sequence using the mussa
+`annotation file format`_ and can be loaded by selecting the
+annotation file when defining a new analysis (see `Create a new
+analysis`_ section) or by defining a .mupa file pointing to your
+annotation file (see `Load a mussa parameter file`_ section).
+
Motifs
~~~~~~
Load Motifs from File
*********************
Motifs
~~~~~~
Load Motifs from File
*********************
+It is possible to load motifs from a file which was saved from a
+previous run or by defining your own motif file. See the `Motif File
+Format`_ section for details.
+
+To load a motif file, select **Load Motif List** item from the
+**File** menu and select a motif list file.
+
+.. image:: images/load_motif.png
+ :alt: Load Motif List
+ :align: center
+
+
+Save Motifs to File
+*******************
+
+Note: Currently not implemented
+
+
Motif Dialog
************
Motif Dialog
************
+FIXME: Continue here.
Detailed Info
-------------
Detailed Info
-------------
@@
-501,7
+529,15
@@
Annotation File Format
~~~~~~~~~~~~~~~~~~~~~~
The first line in the file is the sequence name. Each line there after
~~~~~~~~~~~~~~~~~~~~~~
The first line in the file is the sequence name. Each line there after
-is a **space** seperated annotation.
+is a **space** seperated annotation.
+
+New as of build 198:
+
+ * The annotation format now supports fasta sequences embeded in the
+ annotation file as shown in the format example below. Mussagl will
+ take this sequence and look for an exact match of this sequence in
+ your sequences. If a match is found, it will label it with the name
+ of from the fasta header.
Format:
Format:
@@
-512,6
+548,12
@@
Format:
<start> <stop> <annotation_name> <annotation_type>
<start> <stop> <annotation_name> <annotation_type>
<start> <stop> <annotation_name> <annotation_type>
<start> <stop> <annotation_name> <annotation_type>
<start> <stop> <annotation_name> <annotation_type>
<start> <stop> <annotation_name> <annotation_type>
+ >Fasta Header
+ ACTGACTGACGTACGTAGCTAGCTAGCTAGCACG
+ ACGTACGTACGTACGTAGCTGTCATACGCTAGCA
+ TGCGTAGAGGATCTCGGATGCTAGCGCTATCGAT
+ ACGTACGGCAGTACGCGGTCAGA
+ <start> <stop> <annotation_name> <annotation_type>
...
Example:
...
Example:
@@
-522,6
+564,8
@@
Example:
251 500 Glorp Glorptype
751 1000 Glorp Glorptype
1251 1500 Glorp Glorptype
251 500 Glorp Glorptype
751 1000 Glorp Glorptype
1251 1500 Glorp Glorptype
+ >My favorite DNA sequence
+ GATTACA
1751 2000 Glorp Glorptype
1751 2000 Glorp Glorptype