From: Brandon King Date: Thu, 21 Sep 2006 00:57:33 +0000 (+0000) Subject: Mussagl Manual: Spelling and Grammar Fixes X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=8a5929b88ada08fec0c430cad48f877652c72419 Mussagl Manual: Spelling and Grammar Fixes * Made some spelling and error fixes thanks... Thanks Erich! --- diff --git a/doc/manual/mussagl_manual.rst b/doc/manual/mussagl_manual.rst index 19b9690..79f0c33 100644 --- a/doc/manual/mussagl_manual.rst +++ b/doc/manual/mussagl_manual.rst @@ -5,7 +5,7 @@ Mussagl Manual Brandon W. King --------------- -Last updated: July 7th, 2006 +Last updated: Sept 20th, 2006 Updated to Mussagl build: 287 @@ -18,7 +18,7 @@ Updated to Mussagl build: 287 * Add toggle to genomes. * Document why one fast record per region. * How to deal with the hazards of small utrs vis motif finder. (Add warning) - * Add warning about saving fasta file. + * Add warning about saving FASTA file. * Add a general principles section near the top * Using comparison algorithm which will pickup all repeats * Add info about repeatmasking @@ -28,9 +28,9 @@ Updated to Mussagl build: 287 * Mention advantages of using mupa. * Mention the difference between using arrows and scroll bar * Document the color for motifs - * Update for Mac user left click + * Update for Mac user left-click -* Wormbase/Flybase/mirBASE + * Wormbase/Flybase/mirBASE tutorials @@ -71,7 +71,7 @@ Mussagl C++/Qt/OpenGL ~~~~~~~~~~~~~~~~~~~~~ Refactored version using the more elegant Qt GUI framework and -OpenGL for hardware acceleration for those who have beter graphics +OpenGL for hardware acceleration for those who have better graphics cards. Getting Mussagl @@ -145,7 +145,7 @@ Obtaining Input Data If you already have your data, you can skip ahead to the the `Using Mussagl`_ section. -Lets say you have a gene of interest called 'SMN1' and you want to +Let's say you have a gene of interest called 'SMN1' and you want to know how the sequence surrounding the gene in multiple species is conserved. Guess what, that's what we are going to do, retrieve the DNA sequence for SMN1 and prepare it for using in Mussa. @@ -157,11 +157,11 @@ UCSC Genome Browser Method -------------------------- There are many methods of retrieving DNA sequence, but for this -example we will retrieve SMN1 through the UCSC genome broswer located +example we will retrieve SMN1 through the UCSC genome browser located at http://genome.ucsc.edu/. .. image:: images/ucsc_genome_browser_home.png - :alt: UCSC Genome Broswer + :alt: UCSC Genome Browser :align: center Step 1 - Find SMN1 @@ -218,7 +218,7 @@ Now we have found the location of SMN1 on human! Step 2 - Download CDS/UTR sequence for annotations ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Since we have found **SMN1**, this would be a convient time to extract +Since we have found **SMN1**, this would be a convenient time to extract the DNA sequence for the CDS and UTRs of the gene to use it as an annotation_ in Mussa. @@ -253,22 +253,22 @@ below): 1. UNcheck **introns**. (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). + 2. Select **one FASTA record** per **region**. + (Mussa needs each CDS and UTR represented by one FASTA record per CDS/UTR). 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 :align: center -Now click the **submit** button. You will then see a fasta file with -many fasta records representing the CDS and UTRS. +Now click the **submit** button. You will then see a FASTA file with +many FASTA records representing the CDS and UTRS. .. image:: images/ucsc_gb_smn1_human_get_genomic_sequence_submit.png :alt: Genome Browser - SMN1 (human) - CDS/UTR sequence :align: center -Now you need to save the fasta records to a **text file**. If you are +Now you need to save the FASTA records to a **text file**. If you are using **Firefox** or **Internet Explorer 6+** click on the **File > Save As** menu option. @@ -282,7 +282,7 @@ Type in **smn1_human_annot.txt** for the file name. :align: center **IMPORTANT:** You should open the file with a text editor and make - sure **no html** was saved... If you find any html markup, delete + sure **no HTML** was saved... If you find any HTML markup, delete the markup and save the file. Now we are going to **modify the file** you just saved to **add the @@ -296,7 +296,7 @@ shown below: You can add more annotations to this file if you wish. See the `annotation file format`_ section for details of the file format. By -including fasta records in the annotation_ file, Mussa searches your +including FASTA records in the annotation_ file, Mussa searches your DNA sequence for an exact match of the sequence in the annotation_ file. If found, it will be marked as an annotation_ within Mussa. @@ -325,8 +325,8 @@ screenshot below.) :alt: Genome Browser - SMN1 (human) - DNA Option :align: center -Now in the **get dna in window** page, lets add an arbitrary amount of -extra sequence on to each end of the gene, lets say 5000 base pairs. +Now in the **get dna in window** page, let's add an arbitrary amount of +extra sequence on to each end of the gene, let's say 5000 base pairs. .. image:: images/ucsc_gb_smn1_human_get_dna.png :alt: Genome Browser - SMN1 (human) - Get DNA @@ -350,13 +350,13 @@ Step 4 - Same/similar/related gene other species. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ What good is a multiple sequence alignment viewer without multiple -sequences? Lets find a similar gene in a few more species. +sequences? Let'S find a similar gene in a few more species. Use the back button on your web browser until you get the **genome -broswer view** of **SMN1** as shown below. +browser view** of **SMN1** as shown below. .. image:: images/ucsc_genome_browser_home.png - :alt: UCSC Genome Broswer + :alt: UCSC Genome Browser :align: center **Click on SMN1** shown **between** the **two orange arrows** shown @@ -678,7 +678,7 @@ Dynamic Threshold :alt: Dynamic Threshold :align: center -You can dynamically change the threshold for how strong of match you +You can dynamically change the threshold for how strong a match you consider the conservation to be with one of two options: 1. Number of base pair matches out of window size. @@ -782,7 +782,7 @@ the motif is displayed or not. :alt: Motif Dialog :align: center -Now lets make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide +Now let's make a motif **'AT[C or G]CT'**. Using the `IUPAC Nucleotide Code`_, type in **'ATSCT'** into the first box and 'My Motif' for the name in the second box as shown below. @@ -816,8 +816,8 @@ After Motif: :align: center -View Mussa Alignements ----------------------- +View Mussa Alignments +--------------------- Mussagl allows you to zoom in on Mussa alignments by selecting the set of alignment(s) of interest. To do this, move the mouse near the @@ -827,8 +827,8 @@ side of the conservation track so that you see a bounding box overlaping the alienment(s) of interest and then **let go** of the *left mouse button*. -In the example below, I started by left clicking on the area marked by -a red dot (upper left corner of bounding box) and draging the mouse to +In the example below, I started by left-clicking on the area marked by +a red dot (upper left corner of bounding box) and dragging the mouse to the area marked by a blue dot (lower right corner of the bounding box) and letting go of the left mouse button. @@ -890,8 +890,8 @@ 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**. + * 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 @@ -933,7 +933,7 @@ needs and input sequence. Sequences ~~~~~~~~~ -Mussa reads in sequences which are formatted in the fasta_ +Mussa reads in sequences which are formatted in the FASTA_ format. Mussa may take a long time to run (>10 minutes) if the total bp length near 280Kb. Once mussa has run once, you can reload previously run analyzes. @@ -967,18 +967,18 @@ Parameter File Format SEQUENCE_NUM # first sequence info - SEQUENCE + SEQUENCE ANNOTATION SEQ_START # the second sequence info - SEQUENCE + SEQUENCE # ANNOTATION SEQ_START # SEQ_END # third sequence info - SEQUENCE + SEQUENCE # ANNOTATION # analyzes parameters: command line args -w -t will override these @@ -995,13 +995,13 @@ Parameter File Format "APPEND_THRES", "true or false", "?", "?", "Appends _t## to ANA_NAME" "SEQUENCE_NUM", "integer", "N/A", "true", "The number of sequences to analyze" - "SEQUENCE", "/fasta/filepath.fa", "N/A", "true", "Must define one + "SEQUENCE", "/FASTA/filepath.fa", "N/A", "true", "Must define one sequence per SEQUENCE_NUM." "ANNOTATION", "/annotation/filepath.txt", "N/A", "false", "Optional annotation file. See `annotation file format`_ section for more information." - "SEQ_START", "integer", "1", "false", "Optional index into fasta file" - "SEQ_END", "integer", "1", "false", "Optional index into fasta file" + "SEQ_START", "integer", "1", "false", "Optional index into FASTA file" + "SEQ_END", "integer", "1", "false", "Optional index into FASTA file" "WINDOW", "integer", "N/A", "true", "`Window Size`_" "THRESHOLD", "integer", "N/A", "true", "`Threshold`_" @@ -1015,11 +1015,11 @@ is a **space** separated annotation. New as of build 198: - * The annotation format now supports fasta sequences embedded in the + * The annotation format now supports FASTA sequences embedded 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. + of from the FASTA header. Format: @@ -1030,7 +1030,7 @@ Format: - >Fasta Header + >FASTA Header ACTGACTGACGTACGTAGCTAGCTAGCTAGCACG ACGTACGTACGTACGTAGCTGTCATACGCTAGCA TGCGTAGAGGATCTCGGATGCTAGCGCTATCGAT @@ -1102,5 +1102,5 @@ N G or A or T or C aNy .. _GPL: http://www.opensource.org/licenses/gpl-license.php .. _wiki: http://mussa.caltech.edu .. _build: http://woldlab.caltech.edu/cgi-bin/mussa/wiki/MussaglBuild -.. _fasta: http://en.wikipedia.org/wiki/FASTA_format +.. _FASTA: http://en.wikipedia.org/wiki/fasta_format .. _wpDnaMotif: http://en.wikipedia.org/wiki/DNA_motif \ No newline at end of file