Page History

...

<center>
  <img src="/wiki/download/attachments/2523429/pic20.png"/>
</center>

1. <b>Nucleotide  Nucleotide or protein sequence</b> sequences (Sequence View). If you choose a file with a nucleic or protein sequence you can see the following picture with open a sequence the following views are available: the project view with your documentdocuments, the sequence view with your sequence and its annotations, options panel with many available optionsadditional info and algorithms. You can also use algorithms and instruments from the context menu or the toolbar: 

<center>
  <img src="/wiki/download/attachments/2523429/pic4_1.png"/>
</center>

Example 1: For example, you want to find Finding open reading frames (ORFs) in your sequence. For this select Select the Analyze-->Find ORFs item from the context menu:

<center>
  <img src="/wiki/download/attachments/2523429/pic6.png"/>
</center>

or by Or click on the Show ORFs button on the toolbar Show ORFs icon :

<center>
  <img src="/wiki/download/attachments/2523429/pic7.png"/>
</center>

...

<center>
  <img src="/wiki/download/attachments/2523429/pic8_1.png"/>
</center>

2. If Multiple sequence alignment (MSA Editor).  If you open a file with a multiple sequence alignment you can see the following picture where there are Options Panel, Toolbar and context menu with many instruments and algorithms:views are available: the project view with your documents, the MSA Editor with your alignment, options panel with additional info and algorithms. You can also use algorithms and instruments from the context menu or the toolbar: 

<center>
  <img src="/wiki/download/attachments/2523429/pic5.png"/>
</center>

Example 2: For example, you may want to build Build a tree from your alignment. You can do this by three different ways:

...

<center>
  <img src="/wiki/download/attachments/2523429/pic11.png"/>
</center>

When you choose After calculation the building tree parameters appears in the dialogs the tree appearsMSA Editor in a separate window:

<center>
  <img src="/wiki/download/attachments/2523429/pic12.png"/>
</center>

3. SAM/BAM files (Assembly Browser). If you click open a file with a short reads assembly, like BAM or SAM format files you see the following picture:

<center>
  <img src="/wiki/download/attachments/2523429/pic13.png"/>
</center>

Example 3: For example, you want to highlight Highlighting the strand direction of reads. You can do this by two ways: by using the context menu or by the Options Panel menu.

<center>
  <img src="/wiki/download/attachments/2523429/pic14 (3).png"/>
</center>

 These were the basic functions provided for you by UGENE. Read more about advanced options in the next chapter.