Team:UC Berkeley Tools/Project/Tutorial/SequenceView

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     Now that  we've got it everything looking spiffy, let's try out one of the main view of  the tool - the Sequence View.  On the  main toolbar select &quot;Sequence View&quot; from the View drop down menu.  This should bring up the Sequence View  window.  From here you have many options  - you can load a sequence from a GenBank or FASTA file, drag in a sequence from  another connection, copy and paste your chosen sequence, or enter it  manually.  Let's try opening a GenBank  file ([http://openwetware.org/images/3/39/JCAseq_pSB1A2-Bca9128.str like this one], for  example).  Go to File, and select 'Load  Sequence File' - this should bring up a window allowing you to choose what file  you want to open.  Go to the directory  you saved the file to, select it, and click open (if the directory has many  files in it, you can go to the 'Files of Type' drop down menu and filter it to  only show GenBank or FASTA files).  This  will load the sequence into the current Sequence View window.  From here, you can edit the sequence or  perform a number of operations on it.  But first, let's try adding some informative highlights to this plain  text sequence.  Go to the Highlighting menu,  and select &quot;Open Feature Library Connection&quot;.</p>
     Now that  we've got it everything looking spiffy, let's try out one of the main view of  the tool - the Sequence View.  On the  main toolbar select &quot;Sequence View&quot; from the View drop down menu.  This should bring up the Sequence View  window.  From here you have many options  - you can load a sequence from a GenBank or FASTA file, drag in a sequence from  another connection, copy and paste your chosen sequence, or enter it  manually.  Let's try opening a GenBank  file ([http://openwetware.org/images/3/39/JCAseq_pSB1A2-Bca9128.str like this one], for  example).  Go to File, and select 'Load  Sequence File' - this should bring up a window allowing you to choose what file  you want to open.  Go to the directory  you saved the file to, select it, and click open (if the directory has many  files in it, you can go to the 'Files of Type' drop down menu and filter it to  only show GenBank or FASTA files).  This  will load the sequence into the current Sequence View window.  From here, you can edit the sequence or  perform a number of operations on it.  But first, let's try adding some informative highlights to this plain  text sequence.  Go to the Highlighting menu,  and select &quot;Open Feature Library Connection&quot;.</p>
[[Image:Tut3b.PNG|center]] <p>&nbsp;</p>
[[Image:Tut3b.PNG|center]] <p>&nbsp;</p>
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    <p><strong>6)  Sequence View II</strong><br />
 
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      Now let's  play with some of the other basic tools in the Sequence View.  Try pressing  First, let's find an open reading frame - place your cursor  anywhere in the sequence, go to the &quot;ORFs&quot; menu and select &quot;Find  Next ORF&quot;.  Alternatively, you can  use the shortcut and press [Ctrl + .].  This will place line a light green line underneath the next open reading  frame found in the sequence after the cursor (if other alternate start codons  are enabled in the preferences, their reading frames will be shown using yellow  or red lines).  Highlight this sequence  with the mouse and select the &quot;Translate&quot; option from the  &quot;Tools&quot; menu (or press [Ctrl + T]).  The protein translation of this reading frame will be printed to the  'Output Data' window.  Similiarly, if  you select &quot;Reverse Complement&quot; [Ctrl + /], the reverse complement of  the sequence will be printed.  &quot;Find Reverse ORF&quot; and &quot;Reverse Translate&quot; operate  in the same fashion, but they look at the reverse complement of the  sequence.  &quot;UPPER CASE&quot;,  &quot;Switch Case&quot;, and &quot;lower case&quot; all operate on any portion  of the sequence you care to highlight (case has no effect on sequence analysis  and is treated as aesthetic).  Highlighting a string of nucleotides also displays information like G-C content and melting temperature.  Additionally, you can open up a tools menu under &quot;Tools&quot; [Ctrl + F] to peform find and  replace operations on the sequence.  Let's leave the Sequnce View for now - either select &quot;Exit Sequence  View&quot; from the File menu or click the 'X' in the corner and select  &quot;Yes close&quot; from the resulting pop-up box.</p>
 
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[[Image:Tut6.PNG|center]] <p>&nbsp;</p>
 

Revision as of 01:35, 24 October 2008

Clotho Title small.png


 

Clotho Tutorial

 



3) Sequence View I
Now that we've got it everything looking spiffy, let's try out one of the main view of the tool - the Sequence View. On the main toolbar select "Sequence View" from the View drop down menu. This should bring up the Sequence View window. From here you have many options - you can load a sequence from a GenBank or FASTA file, drag in a sequence from another connection, copy and paste your chosen sequence, or enter it manually. Let's try opening a GenBank file ([http://openwetware.org/images/3/39/JCAseq_pSB1A2-Bca9128.str like this one], for example). Go to File, and select 'Load Sequence File' - this should bring up a window allowing you to choose what file you want to open. Go to the directory you saved the file to, select it, and click open (if the directory has many files in it, you can go to the 'Files of Type' drop down menu and filter it to only show GenBank or FASTA files). This will load the sequence into the current Sequence View window. From here, you can edit the sequence or perform a number of operations on it. But first, let's try adding some informative highlights to this plain text sequence. Go to the Highlighting menu, and select "Open Feature Library Connection".

Tut3b.PNG

 

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