8 Last updated: Oct 17th, 2006
10 Updated to Mussagl build: (In process to 424)
14 * New features / change log
15 * Comment out anything isn't implemented yet.
16 * (DONE) List of features that will be implemented in the future.
17 * Look into the homology mapping of UCSC.
18 * Add toggle to genomes.
19 * Document why one fast record per region.
20 * How to deal with the hazards of small utrs vis motif finder. (Add warning)
21 * Add warning about saving FASTA file.
22 * Add a general principles section near the top
23 * Using comparison algorithm which will pickup all repeats
24 * Add info about repeatmasking
25 * Checking upstream and downstream genes for make sure you are in the right regions.
26 * Later on: look into Ensembl
27 * Look into method of homology instead of blating.
28 * Mention advantages of using mupa.
29 * Mention the difference between using arrows and scroll bar
30 * Document the color for motifs
31 * Update for Mac user left-click
33 * Wormbase/Flybase/mirBASE tutorials
46 * Analysis "Save As" feature
51 .. INSERT CHANGE LOG HERE
52 .. END INSERT CHANGE LOG
54 Features to be Implemented
55 --------------------------
57 * Motif editor supporting more than 10 motifs
58 (Status: http://woldlab.caltech.edu/cgi-bin/mussa/ticket/122)
59 * Save motifs from Mussagl
60 (Status: http://woldlab.caltech.edu/cgi-bin/mussa/ticket/133)
62 For an up-to-date list of features to be implemented visit:
63 http://woldlab.caltech.edu/cgi-bin/mussa/roadmap
72 Mussa is an N-way version of the FamilyRelations (which is a part of
73 the Cartwheel project) 2-way comparative sequence analysis
74 software. Given DNA sequence from N species, Mussa uses all possible
75 pairwise comparions to derive an N-wise comparison. For example, given
76 sequences 1,2,3, and 4, Mussa makes 6 2-way comparisons: 1vs2, 1vs3,
77 1vs4, 2vs3, 2vs4, and 3vs4. It then compares all the links between
78 these comparisons, saving those that satisfy a transitivity
79 requirement. The saved paths are then displayed in an interactive
82 Short History of Mussa
83 ----------------------
85 Mussa Python/PMW Prototype
86 ~~~~~~~~~~~~~~~~~~~~~~~~~~
88 First Python/PMW based protoype.
93 A rewrite for speed purposes using C++ and FLTK GUI toolkit.
98 Refactored version using the more elegant Qt GUI framework and
99 OpenGL for hardware acceleration for those who have better graphics
108 Mussagl has been released open source under the `GPL v2
116 You have the option of building from source or downloading prebuilt
117 binaries. Most people will want the prebuilt versions.
121 * Mac OS X (binary or source)
122 * Windows XP (binary or source)
128 Mussagl in binary form for OS X and Windows and/or source can be
129 downloaded from http://mussa.caltech.edu/.
136 Once you have downloaded the .dmg file, double click on it and follow
137 the install instructions.
139 FIXME: Mention how to launch the program.
144 Once you have downloaded the Mussagl installer, double click on the
145 installer and follow the install instructions.
147 To start Mussagl, launch the program from Start > Programs > Mussagl >
153 Currently we do not have a binary installer for Linux. You will have
154 to build from source. See the 'build from source' section below.
160 Instructions for building from source can be found `build page
161 <http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild>`_ on the
170 If you already have your data, you can skip ahead to the the `Using
173 Let's say you have a gene of interest called 'SMN1' and you want to
174 know how the sequence surrounding the gene in multiple species is
175 conserved. Guess what, that's what we are going to do, retrieve the
176 DNA sequence for SMN1 and prepare it for using in Mussa.
178 For more information about SMN1 visit `NCBI's OMIM
179 <http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
181 The SMN1 data retrieved in this section can be downloaded from the
183 <http://woldlab.caltech.edu/cgi-bin/mussa/wiki/ExampleData>`_ page if
184 you prefer to skip this section of the manual.
187 UCSC Genome Browser Method
188 --------------------------
190 There are many methods of retrieving DNA sequence, but for this
191 example we will retrieve SMN1 through the UCSC genome browser located
192 at http://genome.ucsc.edu/.
195 .. image:: images/ucsc_genome_browser_home.png
196 :alt: UCSC Genome Browser
202 The first step in finding SMN1 is to use the **Gene Sorter** menu
203 option which I have highlighted in orange below:
205 .. image:: images/ucsc_menu_bar_gene_sorter.png
206 :alt: Gene Sorter Menu Option
211 .. image:: images/ucsc_gene_sorter.png
215 We will start by looking for SMN1 in the **Human Genome** and **sorting by name similarity**.
217 .. image:: images/ucsc_gs_sort_name_sim.png
218 :alt: Gene Sorter - Name Similarity
221 After you have selected **Human Genome** and **sorting by name similarity**, type *SMN1* into the search box.
223 .. image:: images/ucsc_gs_smn1.png
227 Press **Go!** and you should see the following page:
229 .. image:: images/ucsc_gs_found.png
233 Click on **SMN1** and you will be taking the gene expression atlas
236 .. image:: images/ucsc_gs_genome_position.png
237 :alt: Gene expression atlas
240 Click on **chr5 70,270,558** found in the **SMN1 row**, **Genome
243 Now we have found the location of SMN1 on human!
245 .. image:: images/ucsc_gb_smn1_human.png
246 :alt: Genome Browser - SMN1 (human)
250 Step 2 - Download CDS/UTR sequence for annotations
251 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
253 Since we have found **SMN1**, this would be a convenient time to extract
254 the DNA sequence for the CDS and UTRs of the gene to use it as an
255 annotation_ in Mussa.
257 **Click on SMN1** shown **between** the **two orange arrows** shown
260 .. image:: images/ucsc_gb_smn1_human_click_smn1.png
261 :alt: Genome Browser - SMN1 (human) - Orange Arrows
264 You should find yourself at the SMN1 description page.
266 .. image:: images/ucsc_gb_smn1_description_page.png
267 :alt: Genome Browser - SMN1 (human) - Description page
270 **Scroll down** until you get to the **Sequence section** and click on
271 **Genomic (chr5:70,256,524-70,284,592)**.
273 .. image:: images/ucsc_gb_smn1_human_sequence.png
274 :alt: Genome Browser - SMN1 (human) - Sequence
277 You should now be at the **Genomic sequence near gene** page:
279 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence.png
280 :alt: Genome Browser - SMN1 (human) - Get genomic sequence
283 Make the following changes (highlighted in orange in the screenshot
286 1. UNcheck **introns**.
287 (We only want to annotate CDS and UTRs.)
288 2. Select **one FASTA record** per **region**.
289 (Mussa needs each CDS and UTR represented by one FASTA record per CDS/UTR).
290 3. Select **CDS in upper case, UTR in lower case.**
292 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png
293 :alt: Genome Browser - SMN1 (human) - Get genomic sequence setup
296 Now click the **submit** button. You will then see a FASTA file with
297 many FASTA records representing the CDS and UTRS.
299 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_submit.png
300 :alt: Genome Browser - SMN1 (human) - CDS/UTR sequence
303 Now you need to save the FASTA records to a **text file**. If you are
304 using **Firefox** or **Internet Explorer 6+** click on the **File >
305 Save As** menu option.
307 **IMPORTANT:** Make sure you select **Text Files** and **NOT**, I
308 repeat **NOT Webpage Complete** (see screenshot below.)
310 Type in **smn1_human_annot.txt** for the file name.
312 .. image:: images/smn1_human_annot.png
313 :alt: Genome Browser - SMN1 (human) - sequence annotation file
316 **IMPORTANT:** You should open the file with a text editor and make
317 sure **no HTML** was saved... If you find any HTML markup, delete
318 the markup and save the file.
320 Now we are going to **modify the file** you just saved to **add the
321 name of the species** to the **annotation file**. All you have to do
322 is **add a new line** at the **top of the file** with the word **'Human'** as
325 .. image:: images/smn1_human_annot_plus_human.png
326 :alt: Genome Browser - SMN1 (human) - sequence annotation file
329 You can add more annotations to this file if you wish. See the
330 `annotation file format`_ section for details of the file format. By
331 including FASTA records in the annotation_ file, Mussa searches your
332 DNA sequence for an exact match of the sequence in the annotation_
333 file. If found, it will be marked as an annotation_ within Mussa.
336 Step 3 - Download gene and upstream/downstream sequence
337 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
339 Use the back button in your web browser to get back the **genome
340 browser view** of **SMN1** as shown below.
342 .. image:: images/ucsc_gb_smn1_human.png
343 :alt: Genome Browser - SMN1 (human)
346 There are two options for getting additional sequence around your
347 gene. The more complex way is to zoom out so that you have the
348 sequence you want being shown in the genome browser and then follow
349 the directions for the following method.
351 The second option, which we will choose, is to leave the genome
352 browser zoomed exactly at the location of SMN1 and click on the
353 **DNA** option on the menu bar (shown with orange arrows in the
356 .. image:: images/ucsc_gb_smn1_human_dna_option.png
357 :alt: Genome Browser - SMN1 (human) - DNA Option
360 Now in the **get dna in window** page, let's add an arbitrary amount of
361 extra sequence on to each end of the gene, let's say 5000 base pairs.
363 .. image:: images/ucsc_gb_smn1_human_get_dna.png
364 :alt: Genome Browser - SMN1 (human) - Get DNA
367 Click the **get DNA** button.
369 .. image:: images/ucsc_gb_smn1_human_dna.png
370 :alt: Genome Browser - SMN1 (human) - DNA
373 Save the DNA sequence to a text file called 'smn1_human_dna.fa' as we
374 did in step 2 with the annotation file.
376 **IMPORTANT:** Make sure the file is saved as a text file and not an
377 HTML file. Open the file with a text editor and remove any HTML markup
381 Step 4 - Same/similar/related gene other species.
382 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
384 What good is a multiple sequence alignment viewer without multiple
385 sequences? Let'S find a similar gene in a few more species.
387 Use the back button on your web browser until you get the **genome
388 browser view** of **SMN1** as shown below.
390 .. image:: images/ucsc_genome_browser_home.png
391 :alt: UCSC Genome Browser
394 **Click on SMN1** shown **between** the **two orange arrows** shown
397 .. image:: images/ucsc_gb_smn1_human_click_smn1.png
398 :alt: Genome Browser - SMN1 (human) - Orange Arrows
401 You should find yourself at the SMN1 description page.
403 .. image:: images/ucsc_gb_smn1_description_page.png
404 :alt: Genome Browser - SMN1 (human) - Description page
407 **Scroll down** until you get to the **Sequence section** and click on
408 **Protein (262 aa)**.
410 .. image:: images/ucsc_gb_smn1_human_sequence.png
411 :alt: Genome Browser - SMN1 (human) - Sequence
414 Copy the SMN1 protein seqeunce by highlighting it and selecting **Edit
415 > Copy** option from the menu.
417 .. image:: images/smn1_human_protein.png
418 :alt: Genome Browser - SMN1 (human) - Protein
421 Press the back button on the web browser once and then scroll to the
422 top of the page and click on the **BLAT** option on the menu bar
423 (shown below with orange arrows).
425 .. image:: images/ucsc_gb_smn1_human_blat.png
426 :alt: Genome Browser - SMN1 (human) - Blat
429 **Paste** in the **protein sequence** and **change** the **genome** to
430 **mouse** as shown below and then click **submit**.
432 .. image:: images/ucsc_gb_smn1_human_blat_paste.png
433 :alt: Genome Browser - SMN1 (human) - Blat paste protein
436 Notice that we have two hits, one of which looks pretty good at 89.9%
439 .. image:: images/ucsc_gb_smn1_human_blat_hits.png
440 :alt: Genome Browser - SMN1 (human) - Blat hits
443 **Click** on the **brower** link next to the 89.9% match. Notice in
444 the genome browser (shown below) that there is an annotated gene
445 called SMN1 for mouse which matches the line called **your sequence
446 from blat search**. This means we are fairly confidant we found the
447 right location in the mouse genome.
449 .. image:: images/ucsc_gb_smn1_human_blat_to_browser.png
450 :alt: Genome Browser - SMN1 (human) - Blat to browser
453 Follow steps 1 through 3 for mouse and then repeat step 4 with the
454 human protein sequence to find **SMN1** in the following species (if
465 Make sure to save the extended DNA sequence and annotation file for
474 Launch Mussagl... It should look similar to the screen shot below.
476 .. image:: images/opened.png
483 ----------------------
485 Currently there are three ways to load a Mussa experiment.
487 1. `Create a new analysis`_
488 2. `Load a mussa parameter file`_ (.mupa)
489 3. `Load an analysis`_
493 Create a new analysis
494 ~~~~~~~~~~~~~~~~~~~~~
496 To create a new analysis select 'Define analysis' from the 'File'
497 menu. You should see a dialog box similar to the one below. For this
498 demo we will use the example sequences that come with Mussagl.
500 .. image:: images/define_analysis.png
501 :alt: Define Analysis
506 1. **Give the experiment a name**, for this demo, we'll use
507 'demo_w30_t20'. Mussa will create a folder with this name to store
508 the analysis files in once it has been run.
510 2. Choose a threshold_... for this demo **choose 20**. See the
511 Threshold_ section for more detailed information.
513 3. Choose a `window size`_. For this demo **choose 30**.
516 4. Choose the number of sequences_ you would like. For this demo
519 .. image:: images/define_analysis_step1a.png
523 First enter the species name of "Human" in the first "Species" text
524 box. Now click on the 'Browse' button next to the sequence input box
525 and then select /examples/seq/human_mck_pro.fa file. Do the same in
526 the next two sequence input boxes selecting mouse_mck_pro.fa and
527 rabbit_mck_pro.fa as shown below. Make sure to give them a species
528 name as well. Note that you can create annotation files using the
529 mussa `Annotation File Format`_ to add annotations to your sequence.
531 .. image:: images/define_analysis_step2.png
532 :alt: Choose sequences
535 Click the **create** button and in a few moments you should see
536 something similar to the following screen shot.
538 .. image:: images/demo.png
542 By default your analysis is NOT saved. If you try to close an analysis
543 without saving, you will be prompted with a dialog box asking you if
544 you would like to save your analysis. The `Saving`_ section for
545 details on saving your analysis. When saving, choose directory and
546 give the analysis the name **demo_w30_t20**. If you close and reopen
547 Mussagl, you will then be able to load the saved analysis. See `Load
548 an analysis`_ section below for details.
551 Load a mussa parameter file
552 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 If you prefer, you can define your Mussa analysis using the Mussa
555 parameter file. See the `Parameter File Format`_ section for details
556 on creating a .mupa file.
558 Once you have a .mupa file created, load Mussagl and select the **File >
559 Create Analysis from File** menu option. Select the .mupa file and click
562 .. image:: images/load_mupa_menu.png
563 :alt: Load Mussa Parameters
566 If you would like to see an example, you can load the
567 **mck3test.mupa** file in the examples directory that comes with
570 .. image:: images/load_mupa_dialog.png
571 :alt: Load Mussa Parameters Dialog
578 To load a previously run analysis open Mussagl and select the **File >
579 Open Existing Analysis** menu option. Select an analysis **directory** and
582 .. image:: images/load_analysis_menu.png
583 :alt: Load Analysis Menu
592 .. Screen-shot with numbers showing features.
594 .. image:: images/window_overview.png
600 1. `DNA Sequence (Black bars)`_
606 4. `Red conservation tracks`_
608 5. `Blue conservation tracks`_
610 6. `Zoom Factor`_ (Base pairs per pixel)
612 7. `Dynamic Threshold`_
614 8. `Sequence Information Bar`_
616 9. `Sequence Scroll Bar`_
619 DNA Sequence (black bars)
620 ~~~~~~~~~~~~~~~~~~~~~~~~~
622 .. image:: images/sequence_bar.png
626 Each of the black bars represents one of the loaded sequences, in this
627 case the sequence around the gene 'MCK' in human, mouse, and rabbit.
633 .. figure:: images/annotation.png
637 Annotation shown in green on sequence bar.
640 Annotations can be included on any of the sequences using the `Load a
641 mussa parameter file`_ or `Create a new analysis`_ method of loading
642 your sequences. You can define annotations by location or using an
643 exact sub-sequence or a FASTA sequence of the section of DNA you wish
644 to annotate. See the `Annotation File Format`_ section for details.
650 .. figure:: images/motif.png
654 Motif shown in light blue on sequence bar.
656 The only real difference between an annotation and motif in Mussagl is
657 that you can define motifs and choose a color from within the GUI. See
658 the `Motifs`_ section for more information.
661 Red conservation tracks
662 ~~~~~~~~~~~~~~~~~~~~~~~
664 .. figure:: images/conservation_tracks.png
665 :alt: Conservation Tracks
668 Conservations tracks shown as red and blue lines between sequence
671 The **red lines** between the sequence bars represent conservation
672 between the sequences (i.e. not reverse complement matches)
674 The amount of sequence conservation shown will depend on how much your
675 sequences are related and the `dynamic threshold`_ you are using.
678 Blue conservation tracks
679 ~~~~~~~~~~~~~~~~~~~~~~~~
681 .. figure:: images/conservation_tracks.png
682 :alt: Conservation Tracks
685 Conservations tracks shown as red and blue lines between sequence
688 **Blue lines** represent **reverse complement** conservation relative
689 to the sequence attached to the top of the blue line.
691 The amount of sequence conservation shown will depend on how much your
692 sequences are related and the `dynamic threshold`_ you are using.
698 .. image:: images/zoom_factor.png
702 The zoom factor represents the number of base pairs represented per
703 pixel. When you zoom in far enough the sequence will switch from
704 seeing a black bar, representing the sequence, to the actual sequence
705 (well, ASCII representation of sequence).
711 .. image:: images/dynamic_threshold.png
712 :alt: Dynamic Threshold
715 You can dynamically change the threshold for how strong a match you
716 consider the conservation to be by changing the value in the dynamic
719 The value you enter is the minimum number of base pairs that have to
720 be matched in order to be considered conserved. The second number that
721 you can't change is the `window size`_ you used when creating the
722 experiment. The last number is the percent match.
724 See the Threshold_ section for more information.
727 Sequence Information Bar
728 ~~~~~~~~~~~~~~~~~~~~~~~~
730 .. image:: images/seq_info_bar.png
731 :alt: Sequence Information Bar
734 The sequence information bars can be found to the left and right sides
735 of Mussagl. Next to each sequence you will find the following
738 1. Species (If it has been defined)
739 2. Total Size of Sequence
740 3. Current base pair position
742 Note that you can **update the species** text box. Make sure to **save your
743 experiment** after making this change by selecting **File > Save
744 Analysis** from the menu.
749 .. image:: images/scroll_bar.png
750 :alt: Sequence Scroll Bar
753 The scroll bar allows you to scroll through the sequence which is
754 useful when you have zoomed in using the `zoom factor`_.
763 Currently annotations can be added to a sequence using the mussa
764 `annotation file format`_ and can be loaded by selecting the
765 annotation file when defining a new analysis (see `Create a new
766 analysis`_ section) or by defining a .mupa file pointing to your
767 annotation file (see `Load a mussa parameter file`_ section).
772 Load Motifs from File
773 *********************
775 It is possible to load motifs from a file which was saved from a
776 previous run or by defining your own motif file. See the `Motif File
777 Format`_ section for details.
779 NOTE: Valid motif list file extensions are:
784 To load a motif file, select **Load Motif List** item from the
785 **File** menu and select a motif list file.
787 .. image:: images/load_motif.png
788 :alt: Load Motif List
795 Note: Currently not implemented
804 * Allow for toggling individual motifs on and off.
807 * Field added for naming motifs.
809 Mussa has the ability to find lab motifs using the `IUPAC Nucleotide
810 Code`_ for defining a motif. To define a motif, select **Edit > Edit
811 Motifs** menu item as shown below.
813 .. image:: images/view_edit_motifs.png
814 :alt: "View > Edit Motifs" Menu
817 You will see a dialog box appear with a "set motifs" button and 10
818 rows for defining motifs and the color that will be displayed on the
819 sequence. By default all 10 motifs start off as with white as the
820 color. In the image below, I changed the color from white to blue to
821 make it easier to see. The first text box is for the motif and the
822 second box is for the name of the motif. The check box defines whether
823 the motif is displayed or not.
825 .. image:: images/motif_dialog_start.png
829 Now let's make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide
830 Code`_, type in **'ATSCT'** into the first box and 'My Motif' for the
831 name in the second box as shown below.
833 .. image:: images/motif_dialog_enter_motif.png
837 Now choose a color for your motif by clicking on the colored area to
838 the left of the motif. In the image above, you would click on the blue
839 square, but by default the squares will be white. Remember to choose a
840 color that will show up well with a black bar as the background.
842 .. image:: images/color_chooser.png
846 Once you have selected the color for your motif, click on the 'set
847 motifs' button. Notice that if Mussa finds matches to your motif will
848 now show up in the main Mussagl window.
852 .. image:: images/motif_dialog_bar_before.png
853 :alt: Sequence bar before motif
858 .. image:: images/motif_dialog_bar_after.png
859 :alt: Sequence bar after motif
863 View Mussa Alignments
864 ---------------------
866 Mussagl allows you to zoom in on Mussa alignments by selecting the set
867 of alignment(s) of interest. To do this, move the mouse near the
868 alignment you are interested in viewing and then **PRESS** and
869 **HOLD** the **LEFT mouse button** and **drag the mouse** to the other
870 side of the conservation track so that you see a bounding box
871 overlaping the alienment(s) of interest and then **let go** of the
874 In the example below, I started by left-clicking on the area marked by
875 a red dot (upper left corner of bounding box) and dragging the mouse to
876 the area marked by a blue dot (lower right corner of the bounding box)
877 and letting go of the left mouse button.
879 .. image:: images/select_sequence.png
880 :alt: Select Sequence
883 All of the lines which were not selected should be washed out as shown
886 .. image:: images/washed_out.png
887 :alt: Tracks washed out
890 With a selection made, goto the **View** menu and select **View mussa alignment**.
892 .. image:: images/view_mussa_alignment.png
893 :alt: View mussa alignment
896 You should see the alignment at the base-pair level as shown below.
898 .. image:: images/mussa_alignment.png
899 :alt: Mussa alignment
906 To run a sub-analysis **highlight** a section of sequence and *right
907 click* on it and select **Add to subanalysis**. To the same for the
908 sequences shown in orange in the screenshot below. Note that you **are
909 NOT limited** to selecting more than one subsequence from the same
912 .. image:: images/subanalysis_select_seqs.png
913 :alt: Subanalysis sequence selection
916 Once you have added your sequences for subanalysis, choose a `window size`_ and `threshold`_ and click **Ok**.
918 .. image:: images/subanalysis_dialog.png
919 :alt: Subanalysis Dialog
922 A new Mussa window will appear with the subanalysis of your sequences
923 once it's done running. This may take a while if you selected large
924 chunks of sequence with a loose threshold.
926 .. image:: images/subanalysis_done.png
927 :alt: Subalaysis complete
931 Copying sequence to clipboard
932 -----------------------------
934 To copy a sequence to the clipboard, highlight a section of sequence,
935 as shown in the screen shot below, and do one of the following:
937 * Select **Copy as FASTA** from the **Edit** menu.
938 * **Right-Click (Left-click + Apple/Command Key on Mac)** on the highlighted sequence and select **Copy as FASTA**.
939 * Press **Ctrl + C (on PC)** or **Apple/Command Key + C (on Mac)** on the keyboard.
941 .. image:: images/copy_sequence.png
946 ---------------------------------
948 * Updated to build 419.
950 To save your current mussa view to an image, select **File > Save to
951 image...** as shown below.
953 .. image:: images/save_to_image_menu.png
954 :alt: File > Save to image...
957 You can define the width and the height of the image to save. By
958 default it will use the same size of your current view. Since the
959 Mussa view is implemented using vectors, if you choose a larger size
960 then your current view, Mussa will redraw at the higher resolution
961 when saving. In other words, you get higher quality images when saving
962 at a higher resolution.
964 If you check the "Lock aspect ratio" check box, which I have circled
965 in red, then when you change one value, say width, the other, height,
966 will update automatically to keep the same aspect ratio.
968 .. image:: images/save_to_image_dialog.png
969 :alt: Save to image dialog
972 Click save and choose a location and filename for your file.
974 The valid image formats are:
976 * .png (default if no extension specified.)
986 The threshold of an analysis is in minimum number of base pair matches
987 must be meet to in order to be kept as a match. Note that you can vary
988 the threshold from within Mussagl. For example, if you choose a
989 `window size`_ of **30** and a **threshold** of **20** the mussa nway
990 transitive algorithm will store all matches that are 20 out of 30 bp
991 matches or better and pass it on to Mussagl. Mussagl will then allow
992 you to dynamically choose a threshold from 20 to 30 base pairs. A
993 threshold of 30 bps would only show 30 out of 30 bp matches. A
994 threshold of 20 bps would show all matches of 20 out of 30 bps or
995 better. If you would like to see results for matches lower than 20 out
996 of 30, you will need to rerun the analysis with a lower threshold.
1001 The typical sizes people tend to choose are between 20 and 30. You
1002 will likely need to experiment with this setting depending on your
1003 needs and input sequence.
1009 Mussa reads in sequences which are formatted in the FASTA_
1010 format. Mussa may take a long time to run (>10 minutes) if the total
1011 bp length near 280Kb. Once mussa has run once, you can reload
1012 previously run analyzes.
1014 FIXME: We have learned more about how much sequence and how many to
1015 put in Mussagl, this information should be documented here.
1023 Parameter File Format
1024 ~~~~~~~~~~~~~~~~~~~~~
1026 **File Format (.mupa):**
1030 # name of analysis directory and stem for associated files
1031 ANA_NAME <analysis_name>
1033 # if APPEND vars true, a _wXX and/or _tYY added to analysis name
1034 # where XX = WINDOW and YY = THRESHOLD
1035 # Highly recommeded with use of command line override of WINDOW or THRESHOLD
1036 APPEND_WIN <true/false>
1037 APPEND_THRES <true/false>
1039 # how many sequences are being analyzed
1042 # first sequence info
1043 SEQUENCE <FASTA_file_path>
1044 ANNOTATION <annotation_file_path>
1045 SEQ_START <sequence_start>
1047 # the second sequence info
1048 SEQUENCE <FASTA_file_path>
1049 # ANNOTATION <annotation_file_path>
1050 SEQ_START <sequence_start>
1051 # SEQ_END <sequence_end>
1053 # third sequence info
1054 SEQUENCE <FASTA_file_path>
1055 # ANNOTATION <annotation_file_path>
1057 # analyzes parameters: command line args -w -t will override these
1061 .. csv-table:: Parameter File Options:
1062 :header: "Option Name", "Value", "Default", "Required", "Description"
1063 :widths: 30 30 30 30 60
1065 "ANA_NAME", "string", "N/A", "true", "Name of analysis (Also
1066 name of directory where analysis will be saved."
1067 "APPEND_WIN", "true/false", "?", "?", "Appends _w## to ANA_NAME"
1068 "APPEND_THRES", "true or false", "?", "?", "Appends _t## to ANA_NAME"
1069 "SEQUENCE_NUM", "integer", "N/A", "true", "The number of sequences
1071 "SEQUENCE", "/FASTA/filepath.fa", "N/A", "true", "Must define one
1072 sequence per SEQUENCE_NUM."
1073 "ANNOTATION", "/annotation/filepath.txt", "N/A", "false", "Optional
1074 annotation file. See `annotation file format`_ section for more
1076 "SEQ_START", "integer", "1", "false", "Optional index into FASTA file"
1077 "SEQ_END", "integer", "1", "false", "Optional index into FASTA file"
1078 "WINDOW", "integer", "N/A", "true", "`Window Size`_"
1079 "THRESHOLD", "integer", "N/A", "true", "`Threshold`_"
1083 Annotation File Format
1084 ~~~~~~~~~~~~~~~~~~~~~~
1086 The first line in the file is the sequence name. Each line there after
1087 is a **space** separated annotation.
1089 New as of build 198:
1091 * The annotation format now supports FASTA sequences embedded in the
1092 annotation file as shown in the format example below. Mussagl will
1093 take this sequence and look for an exact match of this sequence in
1094 your sequences. If a match is found, it will label it with the name
1095 of from the FASTA header.
1101 <species/sequence_name>
1102 <start> <stop> <annotation_name> <annotation_type>
1103 <start> <stop> <annotation_name> <annotation_type>
1104 <start> <stop> <annotation_name> <annotation_type>
1105 <start> <stop> <annotation_name> <annotation_type>
1107 ACTGACTGACGTACGTAGCTAGCTAGCTAGCACG
1108 ACGTACGTACGTACGTAGCTGTCATACGCTAGCA
1109 TGCGTAGAGGATCTCGGATGCTAGCGCTATCGAT
1110 ACGTACGGCAGTACGCGGTCAGA
1111 <start> <stop> <annotation_name> <annotation_type>
1119 251 500 Glorp Glorptype
1120 751 1000 Glorp Glorptype
1121 1251 1500 Glorp Glorptype
1122 >My favorite DNA sequence
1124 1751 2000 Glorp Glorptype
1127 .. _motif_file_format:
1134 <motif> <red> <green> <blue>
1142 IUPAC Nucleotide Code
1143 ~~~~~~~~~~~~~~~~~~~~~~
1145 For your convenience, below is a table of the IUPAC Nucleotide Code.
1147 The following table is table 1 from "Nomenclature for Incompletely
1148 Specified Bases in Nucleic Acid Sequences" which can be found at
1149 http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html.
1151 ====== ================= ===================================
1152 Symbol Meaning Origin of designation
1153 ====== ================= ===================================
1162 S G or C Strong interaction (3 H bonds)
1163 W A or T Weak interaction (2 H bonds)
1164 H A or C or T not-G, H follows G in the alphabet
1165 B G or T or C not-A, B follows A
1166 V G or C or A not-T (not-U), V follows U
1167 D G or A or T not-C, D follows C
1168 N G or A or T or C aNy
1169 ====== ================= ===================================
1172 .. Define links below
1175 .. _GPL: http://www.opensource.org/licenses/gpl-license.php
1176 .. _wiki: http://mussa.caltech.edu
1177 .. _build: http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild
1178 .. _FASTA: http://en.wikipedia.org/wiki/fasta_format
1179 .. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif