8 Last updated: May 23th, 2006
10 Updated to Mussagl build: 200 (Update to 230 in progress)
23 Short History of Mussa
24 ----------------------
27 Mussa Python/PMW Prototype
28 ~~~~~~~~~~~~~~~~~~~~~~~~~~
45 Mussagl has been released open source under the `GPL v2
53 You have the option of building from source or downloading prebuilt
54 binaries. Most people will want the prebuilt versions.
58 * Mac OS X (binary or source)
59 * Windows XP (binary or source)
65 Mussagl in binary form for OS X and Windows and/or source can be
66 downloaded from http://mussa.caltech.edu/.
73 Once you have downloaded the .dmg file, double click on it and follow
74 the install instructions.
76 FIXME: Mention how to launch the program.
81 Once you have downloaded the Mussagl installer, double click on the
82 installer and follow the install instructions.
84 To start Mussagl, launch the program from Start > Programs > Mussagl >
90 Currently we do not have a binary installer for Linux. You will have
91 to build from source. See the 'build from source' section below.
97 Instructions for building from source can be found `build page
98 <http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild>`_ on the
107 If you already have your data, you can skip ahead to the the `Using
110 Lets say you have a gene of interest called 'SMN1' and you want to
111 know how the sequence surrounding the gene in multiple species is
112 conserved. Guess what, that's what we are going to do, retrieve the
113 DNA sequence for SMN1 and prepare it for using in Mussa.
115 For more information about SMN1 visit `NCBI's OMIM
116 <http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=609682>`_.
118 UCSC Genome Browser Method
119 --------------------------
121 There are many methods of retrieving DNA sequence, but for this
122 example we will retrieve SMN1 through the UCSC genome broswer located
123 at http://genome.ucsc.edu/.
125 .. image:: images/ucsc_genome_browser_home.png
126 :alt: UCSC Genome Broswer
132 The first step in finding SMN1 is to use the **Gene Sorter** menu
133 option which I have highlighted in orange below:
135 .. image:: images/ucsc_menu_bar_gene_sorter.png
136 :alt: Gene Sorter Menu Option
141 .. image:: images/ucsc_gene_sorter.png
145 We will start by looking for SMN1 in the **Human Genome** and **sorting by name similarity**.
147 .. image:: images/ucsc_gs_sort_name_sim.png
148 :alt: Gene Sorter - Name Similarity
151 After you have selected **Human Genome** and **sorting by name similarity**, type *SMN1* into the search box.
153 .. image:: images/ucsc_gs_smn1.png
157 Press **Go!** and you should see the following page:
159 .. image:: images/ucsc_gs_found.png
163 Click on **SMN1** and you will be taking the gene expression atlas
166 .. image:: images/ucsc_gs_genome_position.png
167 :alt: Gene expression atlas
170 Click on **chr5 70,270,558** found in the **SMN1 row**, **Genome
173 Now we have found the location of SMN1 on human!
175 .. image:: images/ucsc_gb_smn1_human.png
176 :alt: Genome Browser - SMN1 (human)
180 Step 2 - Download CDS/UTR sequence for annotations
181 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 Since we have found **SMN1**, this would be a convient time to extract
184 the DNA sequence for the CDS and UTRs of the gene to use it as an
185 annotation_ in Mussa.
187 **Click on SMN1** shown **between** the **two orange arrows** shown
190 .. image:: images/ucsc_gb_smn1_human_click_smn1.png
191 :alt: Genome Browser - SMN1 (human) - Orange Arrows
194 You should find yourself at the SMN1 description page.
196 .. image:: images/ucsc_gb_smn1_description_page.png
197 :alt: Genome Browser - SMN1 (human) - Description page
200 **Scroll down** until you get to the **Sequence section** and click on
201 **Genomic (chr5:70,256,524-70,284,592)**.
203 .. image:: images/ucsc_gb_smn1_human_sequence.png
204 :alt: Genome Browser - SMN1 (human) - Sequence
207 You should now be at the **Genomic sequence near gene** page:
209 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence.png
210 :alt: Genome Browser - SMN1 (human) - Get genomic sequence
213 Make the following changes (highlighted in orange in the screenshot
216 1. UNcheck **introns**.
217 (We only want to annotate CDS and UTRs.)
218 2. Select **one fasta record** per **region**.
219 (Mussa needs each CDS and UTR represented by one fasta record per CDS/UTR).
220 3. Select **split UTR and CDS parts of an exon into separate FASTA records**.
221 (Breaks up **exons** into CDSs and UTRs.)
223 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png
224 :alt: Genome Browser - SMN1 (human) - Get genomic sequence setup
227 Now click the **submit** button. You will then see a fasta file with
228 many fasta records representing the CDS and UTRS.
230 .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_submit.png
231 :alt: Genome Browser - SMN1 (human) - CDS/UTR sequence
234 Now you need to save the fasta records to a **text file**. If you are
235 using **Firefox** or **Internet Explorer 6+** click on the **File >
236 Save As** menu option.
238 **IMPORTANT:** Make sure you select **Text Files** and **NOT**, I
239 repeat **NOT Webpage Complete** (see screenshot below.)
241 Type in **smn1_human_annot.txt** for the file name.
243 .. image:: images/smn1_human_annot.png
244 :alt: Genome Browser - SMN1 (human) - sequence annotation file
247 **IMPORTANT:** You should open the file with a text editor and make
248 sure **no html** was saved... If you find any html markup, delete
249 the markup and save the file.
251 Now we are going to **modify the file** you just saved to **add the
252 name of the species** to the **annotation file**. All you have to do
253 is **add a new line** at the **top of the file** with the word **'Human'** as
256 .. image:: images/smn1_human_annot_plus_human.png
257 :alt: Genome Browser - SMN1 (human) - sequence annotation file
260 You can add more annotations to this file if you wish. See the
261 `annotation file format`_ section for details of the file format. By
262 including fasta records in the annotation_ file, Mussa searches your
263 DNA sequence for an exact match of the sequence in the annotation_
264 file. If found, it will be marked as an annotation_ within Mussa.
267 Step 3 - Download gene and upstream/downstream sequence
268 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
270 Use the back button in your web browser to get back the **genome
271 browser view** of **SMN1** as shown below.
273 .. image:: images/ucsc_gb_smn1_human.png
274 :alt: Genome Browser - SMN1 (human)
277 There are two options for getting additional sequence around your
278 gene. The more complex way is to zoom out so that you have the
279 sequence you want being shown in the genome browser and then follow
280 the directions for the following method.
282 The second option, which we will choose, is to leave the genome
283 browser zoomed exactly at the location of SMN1 and click on the
284 **DNA** option on the menu bar (shown with orange arrows in the
287 .. image:: images/ucsc_gb_smn1_human_dna_option.png
288 :alt: Genome Browser - SMN1 (human) - DNA Option
291 Now in the **get dna in window** page, lets add an arbitrary amount of
292 extra sequence on to each end of the gene, lets say 5000 base pairs.
294 .. image:: images/ucsc_gb_smn1_human_get_dna.png
295 :alt: Genome Browser - SMN1 (human) - Get DNA
298 Click the **get DNA** button.
300 .. image:: images/ucsc_gb_smn1_human_dna.png
301 :alt: Genome Browser - SMN1 (human) - DNA
304 Save the DNA sequence to a text file called 'smn1_human_dna.fa' as we
305 did in step 2 with the annotation file.
307 **IMPORTANT:** Make sure the file is saved as a text file and not an
308 HTML file. Open the file with a text editor and remove any HTML markup
312 Step 4 - Same/similar/related gene other species.
313 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
315 What good is a multiple sequence alignment viewer without multiple
316 sequences? Lets find a similar gene in a few more species.
318 Use the back button on your web browser until you get the **genome
319 broswer view** of **SMN1** as shown below.
321 .. image:: images/ucsc_genome_browser_home.png
322 :alt: UCSC Genome Broswer
325 **Click on SMN1** shown **between** the **two orange arrows** shown
328 .. image:: images/ucsc_gb_smn1_human_click_smn1.png
329 :alt: Genome Browser - SMN1 (human) - Orange Arrows
332 You should find yourself at the SMN1 description page.
334 .. image:: images/ucsc_gb_smn1_description_page.png
335 :alt: Genome Browser - SMN1 (human) - Description page
338 **Scroll down** until you get to the **Sequence section** and click on
339 **Protein (262 aa)**.
341 .. image:: images/ucsc_gb_smn1_human_sequence.png
342 :alt: Genome Browser - SMN1 (human) - Sequence
345 Copy the SMN1 protein seqeunce by highlighting it and selecting **Edit
346 > Copy** option from the menu.
348 .. image:: images/smn1_human_protein.png
349 :alt: Genome Browser - SMN1 (human) - Protein
352 Press the back button on the web browser once and then scroll to the
353 top of the page and click on the **BLAT** option on the menu bar
354 (shown below with orange arrows).
356 .. image:: images/ucsc_gb_smn1_human_blat.png
357 :alt: Genome Browser - SMN1 (human) - Blat
360 **Paste** in the **protein sequence** and **change** the **genome** to
361 **mouse** as shown below and then click **submit**.
363 .. image:: images/ucsc_gb_smn1_human_blat_paste.png
364 :alt: Genome Browser - SMN1 (human) - Blat paste protein
367 Notice that we have two hits, one of which looks pretty good at 89.9%
370 .. image:: images/ucsc_gb_smn1_human_blat_hits.png
371 :alt: Genome Browser - SMN1 (human) - Blat hits
374 **Click** on the **brower** link next to the 89.9% match. Notice in
375 the genome browser (shown below) that there is an annotated gene
376 called SMN1 for mouse which matches the line called **your sequence
377 from blat search**. This means we are fairly confidant we found the
378 right location in the mouse genome.
380 .. image:: images/ucsc_gb_smn1_human_blat_to_browser.png
381 :alt: Genome Browser - SMN1 (human) - Blat to browser
384 Follow steps 1 through 3 for mouse and then repeat step 4 with the
385 human protein sequence to find **SMN1** in the following species (if
396 Make sure to save the extended DNA sequence and annotation file for
405 Launch Mussagl... It should look similar to the screen shot below.
407 .. image:: images/opened.png
414 ----------------------
416 Currently there are three ways to load a Mussa experiment.
418 1. `Create a new analysis`_
419 2. `Load a mussa parameter file`_ (.mupa)
420 3. `Load an analysis`_
424 Create a new analysis
425 ~~~~~~~~~~~~~~~~~~~~~
427 To create a new analysis select 'Define analysis' from the 'File'
428 menu. You should see a dialog box similar to the one below. For this
429 demo we will use the example sequences that come with Mussagl.
431 .. image:: images/define_analysis.png
432 :alt: Define Analysis
437 1. **Give the experiment a name**, for this demo, we'll use
438 'demo_w30_t20'. Mussa will create a folder with this name to store
439 the analysis files in once it has been run.
441 2. Choose a `window size`_. For this demo **choose 30**.
443 3. Choose a threshold_... for this demo **choose 20**. See the
444 Threshold_ section for more detailed information.
446 4. Choose the number of sequences_ you would like. For this demo
449 .. image:: images/define_analysis_step1a.png
453 Now click on the 'Browse' button next to the sequence input box and
454 then select /examples/seq/human_mck_pro.fa file. Do the same in the
455 next two sequence input boxes selecting mouse_mck_pro.fa and
456 rabbit_mck_pro.fa as shown below. Note that you can create annotation
457 files using the mussa `Annotation File Format`_ to add annotations to
460 .. image:: images/define_analysis_step2.png
461 :alt: Choose sequences
464 Click the **create** button and in a few moments you should see
465 something similar to the following screen shot.
467 .. image:: images/demo.png
471 This analysis is now saved in a directory called **demo_w30_t20** in
472 the current working directory. If you close and reopen Mussagl, you
473 can reload the saved analysis. See `Load an analysis`_ section below
477 Load a mussa parameter file
478 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
480 If you prefer, you can define your Mussa analysis using the Mussa
481 parameter file. See the `Parameter File Format`_ section for details
482 on creating a .mupa file.
484 Once you have a .mupa file created, load Mussagl and select the **File >
485 Load Mussa Parameters** menu option. Select the .mupa file and click
488 .. image:: images/load_mupa_menu.png
489 :alt: Load Mussa Parameters
492 If you would like to see an example, you can load the
493 **mck3test.mupa** file in the examples directory that comes with
496 .. image:: images/load_mupa_dialog.png
497 :alt: Load Mussa Parameters Dialog
504 To load a previously run analysis open Mussagl and select the **File >
505 Load Analysis** menu option. Select an analysis **directory** and
508 .. image:: images/load_analysis_menu.png
509 :alt: Load Analysis Menu
518 .. Screen-shot with numbers showing features.
520 .. image:: images/window_overview.png
526 1. `DNA Sequence (Black bars)`_
532 4. `Conservation tracks`_
536 6. `Zoom Factor`_ (Base pairs per pixel)
538 7. `Dynamic Threshold`_
540 8. `Sequence Information Bar`_
542 9. `Sequence Scroll Bar`_
545 DNA Sequence (black bars)
546 ~~~~~~~~~~~~~~~~~~~~~~~~~
548 .. image:: images/sequence_bar.png
552 Each of the black bars represents one of the loaded sequences, in this
553 case the sequence around the gene 'MCK' in human, mouse, and rabbit.
555 FIXME: Should I mention the repeats here?
561 .. figure:: images/annotation.png
565 Annotation shown in green on sequence bar.
568 Annotations can be included on any of the sequences using the `Load a
569 mussa parameter file`_ method of loading your sequences. You can
570 define annotations by location or using an exact sub-sequence and you
571 may also choose any color for display of the annotation; see the
572 `Annotation File Format`_ section for details.
574 Note: Currently there is no way to add annotations using the GUI (only
575 via the .mupa file). We plan to add this feature in the future, but it
576 likely will not make it into the first release.
582 .. figure:: images/motif.png
586 Motif shown in light blue on sequence bar.
588 The only real difference between an annotation and motif in Mussagl is
589 that you can define motifs from within the GUI. See the `Motifs`_
590 section for more information.
596 .. figure:: images/conservation_tracks.png
597 :alt: Conservation Tracks
600 Conservations tracks shown as red and blue lines between sequence
603 The **red lines** between the sequence bars represent conservation
604 between the sequences and **blue lines** represent **reverse
605 complement** conservation. The amount of sequence conservation shown
606 will depend on the relatedness of your sequences and the `dynamic
607 threshold` you are using. Sequences with lots of repeats will cause
608 major slow downs in calculating the matches.
614 .. image:: images/motif_toggle.png
618 Toggles motifs on and off. This will not turn on and off annotations.
620 Note: As of the current build (#200), this feature hasn't been
627 .. image:: images/zoom_factor.png
631 The zoom factor represents the number of base pairs represented per
632 pixel. When you zoom in far enough the sequence will switch from
633 seeing a black bar, representing the sequence, to the actual sequence
634 (well, ASCII representation of sequence).
640 .. image:: images/dynamic_threshold.png
641 :alt: Dynamic Threshold
644 You can dynamically change the threshold for how strong of match you
645 consider the conservation to be with one of two options:
647 1. Number of base pair matches out of window size.
649 2. Percent base pair conservation.
651 See the Threshold_ section for more information.
654 Sequence Information Bar
655 ~~~~~~~~~~~~~~~~~~~~~~~~
657 .. image:: images/seq_info_bar.png
658 :alt: Sequence Information Bar
661 The sequence information bars can be found to the left and right sides
662 of Mussagl. Next to each sequence you will find the following
665 1. Species (If it has been defined)
666 2. Total Size of Sequence
667 3. Current base pair position
673 .. image:: images/scroll_bar.png
674 :alt: Sequence Scroll Bar
677 The scroll bar allows you to scroll through the sequence which is
678 useful when you have zoomed in using the `zoom factor`_.
687 Currently annotations can be added to a sequence using the mussa
688 `annotation file format`_ and can be loaded by selecting the
689 annotation file when defining a new analysis (see `Create a new
690 analysis`_ section) or by defining a .mupa file pointing to your
691 annotation file (see `Load a mussa parameter file`_ section).
696 Load Motifs from File
697 *********************
699 It is possible to load motifs from a file which was saved from a
700 previous run or by defining your own motif file. See the `Motif File
701 Format`_ section for details.
703 To load a motif file, select **Load Motif List** item from the
704 **File** menu and select a motif list file.
706 .. image:: images/load_motif.png
707 :alt: Load Motif List
714 Note: Currently not implemented
720 Mussa has the ability to find lab motifs using the `IUPAC Nucleotide
721 Code`_ for defining a motif. To define a motif, select **View > Edit
722 Motifs** menu item as shown below.
724 .. image:: images/view_edit_motifs.png
725 :alt: "View > Edit Motifs" Menu
728 You will see a dialog box appear with a "set motifs" button and 10
729 rows for defining motifs and the color that will be displayed on the
730 sequence. By default all 10 motifs start off as with white as the
731 color. In the image below, I changed the color from white to blue to
732 make it easier to see.
734 .. image:: images/motif_dialog_start.png
738 Now lets make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide
739 Code`_, type in **'ATSCT'** into the first box as shown below.
741 .. image:: images/motif_dialog_enter_motif.png
745 Now choose a color for your motif by clicking on the colored area to
746 the left of the motif. In the image above, you would click on the blue
747 square, but by default the squares will be white. Remember to choose a
748 color that will show up well with a black bar as the background.
750 .. image:: images/color_chooser.png
754 Once you have selected the color for your motif, click on the 'set
755 motifs' button. Notice that if Mussa finds matches to your motif will
756 now show up in the main Mussagl window.
760 .. image:: images/motif_dialog_bar_before.png
761 :alt: Sequence bar before motif
766 .. image:: images/motif_dialog_bar_after.png
767 :alt: Sequence bar after motif
771 View Mussa Alignements
772 ----------------------
774 Mussagl allows you to zoom in on Mussa alignments by selecting the set
775 of alignment(s) of interest. To do this, move the mouse near the
776 alignment you are interested in viewing and then **PRESS** and
777 **HOLD** the **LEFT mouse button** and **drag the mouse** to the other
778 side of the conservation track so that you see a bounding box
779 overlaping the alienment(s) of interest and then **let go** of the
782 In the example below, I started by left clicking on the area marked by
783 a red dot (upper left corner of bounding box) and draging the mouse to
784 the area marked by a blue dot (lower right corner of the bounding box)
785 and letting go of the left mouse button.
787 .. image:: images/select_sequence.png
788 :alt: Select Sequence
791 All of the lines which were not selected should be washed out as shown
794 .. image:: images/washed_out.png
795 :alt: Tracks washed out
798 With a selection made, goto the **View** menu and select **View mussa alignment**.
800 .. image:: images/view_mussa_alignment.png
801 :alt: View mussa alignment
804 You should see the alignment at the base-pair level as shown below.
806 .. image:: images/mussa_alignment.png
807 :alt: Mussa alignment
814 ---------------------------------
816 FIXME: Need to write this section
825 The threshold of an analysis is in minimum number of base pair matches
826 must be meet to in order to be kept as a match. Note that you can vary
827 the threshold from within Mussagl. For example, if you choose a
828 `window size`_ of **30** and a **threshold** of **20** the mussa nway
829 transitive algorithm will store all matches that are 20 out of 30 bp
830 matches or better and pass it on to Mussagl. Mussagl will then allow
831 you to dynamically choose a threshold from 20 to 30 base pairs. A
832 threshold of 30 bps would only show 30 out of 30 bp matches. A
833 threshold of 20 bps would show all matches of 20 out of 30 bps or
834 better. If you would like to see results for matches lower than 20 out
835 of 30, you will need to rerun the analysis with a lower threshold.
840 The typical sizes people tend to choose are between 20 and 30. You
841 will likely need to experiment with this setting depending on your
842 needs and input sequence.
848 Mussa reads in sequences which are formatted in the fasta_
849 format. Mussa may take a long time to run (>10 minutes) if the total
850 bp length near 280Kb. Once mussa has run once, you can reload
851 previously run analyzes.
853 FIXME: We have learned more about how much sequence and how many to
854 put in Mussagl, this information should be documented here.
862 Parameter File Format
863 ~~~~~~~~~~~~~~~~~~~~~
865 **File Format (.mupa):**
869 # name of analysis directory and stem for associated files
870 ANA_NAME <analysis_name>
872 # if APPEND vars true, a _wXX and/or _tYY added to analysis name
873 # where XX = WINDOW and YY = THRESHOLD
874 # Highly recommeded with use of command line override of WINDOW or THRESHOLD
875 APPEND_WIN <true/false>
876 APPEND_THRES <true/false>
878 # how many sequences are being analyzed
881 # first sequence info
882 SEQUENCE <fasta_file_path>
883 ANNOTATION <annotation_file_path>
884 SEQ_START <sequence_start>
886 # the second sequence info
887 SEQUENCE <fasta_file_path>
888 # ANNOTATION <annotation_file_path>
889 SEQ_START <sequence_start>
890 # SEQ_END <sequence_end>
892 # third sequence info
893 SEQUENCE <fasta_file_path>
894 # ANNOTATION <annotation_file_path>
896 # analyzes parameters: command line args -w -t will override these
900 .. csv-table:: Parameter File Options:
901 :header: "Option Name", "Value", "Default", "Required", "Description"
902 :widths: 30 30 30 30 60
904 "ANA_NAME", "string", "N/A", "true", "Name of analysis (Also
905 name of directory where analysis will be saved."
906 "APPEND_WIN", "true/false", "?", "?", "Appends _w## to ANA_NAME"
907 "APPEND_THRES", "true or false", "?", "?", "Appends _t## to ANA_NAME"
908 "SEQUENCE_NUM", "integer", "N/A", "true", "The number of sequences
910 "SEQUENCE", "/fasta/filepath.fa", "N/A", "true", "Must define one
911 sequence per SEQUENCE_NUM."
912 "ANNOTATION", "/annotation/filepath.txt", "N/A", "false", "Optional
913 annotation file. See `annotation file format`_ section for more
915 "SEQ_START", "integer", "1", "false", "Optional index into fasta file"
916 "SEQ_END", "integer", "1", "false", "Optional index into fasta file"
917 "WINDOW", "integer", "N/A", "true", "`Window Size`_"
918 "THRESHOLD", "integer", "N/A", "true", "`Threshold`_"
922 Annotation File Format
923 ~~~~~~~~~~~~~~~~~~~~~~
925 The first line in the file is the sequence name. Each line there after
926 is a **space** separated annotation.
930 * The annotation format now supports fasta sequences embedded in the
931 annotation file as shown in the format example below. Mussagl will
932 take this sequence and look for an exact match of this sequence in
933 your sequences. If a match is found, it will label it with the name
934 of from the fasta header.
940 <species/sequence_name>
941 <start> <stop> <annotation_name> <annotation_type>
942 <start> <stop> <annotation_name> <annotation_type>
943 <start> <stop> <annotation_name> <annotation_type>
944 <start> <stop> <annotation_name> <annotation_type>
946 ACTGACTGACGTACGTAGCTAGCTAGCTAGCACG
947 ACGTACGTACGTACGTAGCTGTCATACGCTAGCA
948 TGCGTAGAGGATCTCGGATGCTAGCGCTATCGAT
949 ACGTACGGCAGTACGCGGTCAGA
950 <start> <stop> <annotation_name> <annotation_type>
958 251 500 Glorp Glorptype
959 751 1000 Glorp Glorptype
960 1251 1500 Glorp Glorptype
961 >My favorite DNA sequence
963 1751 2000 Glorp Glorptype
966 .. _motif_file_format:
973 <motif> <red> <green> <blue>
981 IUPAC Nucleotide Code
982 ~~~~~~~~~~~~~~~~~~~~~~
984 For your convenience, below is a table of the IUPAC Nucleotide Code.
986 The following table is table 1 from "Nomenclature for Incompletely
987 Specified Bases in Nucleic Acid Sequences" which can be found at
988 http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html.
990 ====== ================= ===================================
991 Symbol Meaning Origin of designation
992 ====== ================= ===================================
1001 S G or C Strong interaction (3 H bonds)
1002 W A or T Weak interaction (2 H bonds)
1003 H A or C or T not-G, H follows G in the alphabet
1004 B G or T or C not-A, B follows A
1005 V G or C or A not-T (not-U), V follows U
1006 D G or A or T not-C, D follows C
1007 N G or A or T or C aNy
1008 ====== ================= ===================================
1011 .. Define links below
1014 .. _GPL: http://www.opensource.org/licenses/gpl-license.php
1015 .. _wiki: http://mussa.caltech.edu
1016 .. _build: http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild
1017 .. _fasta: http://en.wikipedia.org/wiki/FASTA_format
1018 .. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif
projects / mussa.git / blob