From: Brandon King Date: Thu, 6 Jul 2006 20:45:51 +0000 (+0000) Subject: Manual: UCSC Update, Copy sequence, Sub-analysis X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=4c8aa1005db1332af9ae19147d7faf42aca09867 Manual: UCSC Update, Copy sequence, Sub-analysis * Added more screenshots * Updated UCSC Genome Browser sequence retrieval information * Copy sequence to clipboard section added * Subanalysis section added --- diff --git a/doc/manual/images/copy_sequence.png b/doc/manual/images/copy_sequence.png new file mode 100644 index 0000000..6784e53 Binary files /dev/null and b/doc/manual/images/copy_sequence.png differ diff --git a/doc/manual/images/subanalysis_dialog.png b/doc/manual/images/subanalysis_dialog.png new file mode 100644 index 0000000..cacad04 Binary files /dev/null and b/doc/manual/images/subanalysis_dialog.png differ diff --git a/doc/manual/images/subanalysis_done.png b/doc/manual/images/subanalysis_done.png new file mode 100644 index 0000000..b58444c Binary files /dev/null and b/doc/manual/images/subanalysis_done.png differ diff --git a/doc/manual/images/subanalysis_select_seqs.png b/doc/manual/images/subanalysis_select_seqs.png new file mode 100644 index 0000000..24a0b65 Binary files /dev/null and b/doc/manual/images/subanalysis_select_seqs.png differ diff --git a/doc/manual/images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png b/doc/manual/images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png index 66fb295..9f3a5eb 100644 Binary files a/doc/manual/images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png and b/doc/manual/images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png differ diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index f81d689..273e65a 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -5,9 +5,9 @@ Mussagl Manual Brandon W. King --------------- -Last updated: June 12th, 2006 +Last updated: July 7th, 2006 -Updated to Mussagl build: 200 (Update to 230 in progress) +Updated to Mussagl build: 200 (Update to 286 in progress) .. contents:: @@ -19,6 +19,15 @@ Introduction What is Mussagl? ---------------- +Mussa is an N-way version of the FamilyRelations (which is a part of +the Cartwheel project) 2-way comparative sequence analysis +software. Given DNA sequence from N species, Mussa uses all possible +pairwise comparions to derive an N-wise comparison. For example, given +sequences 1,2,3, and 4, Mussa makes 6 2-way comparisons: 1vs2, 1vs3, +1vs4, 2vs3, 2vs4, and 3vs4. It then compares all the links between +these comparisons, saving those that satisfy a transitivity +requirement. The saved paths are then displayed in an interactive +viewer. Short History of Mussa ---------------------- @@ -27,14 +36,19 @@ Short History of Mussa Mussa Python/PMW Prototype ~~~~~~~~~~~~~~~~~~~~~~~~~~ +First Python/PMW based protoype. Mussa C++/FLTK ~~~~~~~~~~~~~~ +A rewrite for speed purposes using C++ and FLTK GUI toolkit. Mussagl C++/Qt/OpenGL ~~~~~~~~~~~~~~~~~~~~~ +Refactored version using the more elegant Qt GUI framework and +OpenGL for hardware acceleration for those who have beter graphics +cards. Getting Mussagl =============== @@ -217,8 +231,7 @@ below): (We only want to annotate CDS and UTRs.) 2. Select **one fasta record** per **region**. (Mussa needs each CDS and UTR represented by one fasta record per CDS/UTR). - 3. Select **split UTR and CDS parts of an exon into separate FASTA records**. - (Breaks up **exons** into CDSs and UTRs.) + 3. Select **CDS in upper case, UTR in lower case.** .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_diff.png :alt: Genome Browser - SMN1 (human) - Get genomic sequence setup @@ -808,7 +821,47 @@ You should see the alignment at the base-pair level as shown below. :align: center +Sub-analysis +------------ +To run a sub-analysis **highlight** a section of sequence and *right +click* on it and select **Add to subanalysis**. To the same for the +sequences shown in orange in the screenshot below. Note that you **are +NOT limited** to selecting more than one subsequence from the same +sequence. + +.. image:: images/subanalysis_select_seqs.png + :alt: Subanalysis sequence selection + :align: center + +Once you have added your sequences for subanalysis, choose a `window size`_ and `threshold`_ and click **Ok**. + +.. image:: images/subanalysis_dialog.png + :alt: Subanalysis Dialog + :align: center + +A new Mussa window will appear with the subanalysis of your sequences +once it's done running. This may take a while if you selected large +chunks of sequence with a loose threshold. + +.. image:: images/subanalysis_done.png + :alt: Subalaysis complete + :align: center + + +Copying sequence to clipboard +----------------------------- + +To copy a sequence to the clipboard, highlight a section of sequence, +as shown in the screen shot below, and do one of the following: + + * Select **Copy as Fasta** from the **Edit** menu. + * **Right Click (Left click + Apple/Command Key on Mac)** on the highlighted sequence and select **Copy as Fasta**. + * Press **Ctrl + C (on PC)** or **Apple/Command Key + C (on Mac)** on the keyboard. + +.. image:: images/copy_sequence.png + :alt: Copy sequence + :align: center Saving to an Image ---------------------------------