Loading protein sequences and alignments into Jalview

Loading protein sequences and alignments into Jalview

Welcome to a Jalview Online Training video,
where I will be explaining the different way to load sequences in Jalview. Hello, I am Suzanne Duce, the Jalview training officer at the College of Life Sciences in the University of Dundee. First we should launch Jalview. This can be done by clicking on the pink web
start button on of the Jalview web site located at www.jalview.org. Or alternatively, it can be opened using the
Jalview JNLP file that was downloaded during web launch. Several windows open as Jalview starts up.
To close these go to the desktop and select the window option. In the drop down menu select Close All. For more information about how to launch Jalview,
check out this video on our Jalview website. There are a number of different ways to load
sequences and sequence alignment into Jalview. If you have data saved in a sequence alignment
format. Then go to the Jalview desktop and select
file in the drop down menu, select input alignment option, and then select from file. This will open another window, locate your
file of interest, and click open and the sequences will load. Jalview can read sequences saved in text files. Drag the file icon from its folder and drop
it on to the Jalview window, this will open the sequences in a new alignment
window. However Jalview can not read documents produced by a word processing program such as Microsoft Word If you drag and drop a word document into
Jalview, you will get an error message. One way to read this data into Jalview is
to open the word document, select the sequence text and copy it in to the clipboard. Then select file option on your desktop, and
select Input Alignment option, but this time chose from textbox. A cut and paste window will appear, paste
the data into the window, and click New Window, and this will to read the data if it is the
appropriate format. Note: If you drag a second file onto the desktop,
it will open in a new alignment window. If you drag the file onto an existing Jalview
alignment window, then the file will be read onto this alignment. Jalview can read sequences and sequence alignments
directly from public databases such as Uniprot, Pfam, RFAM and the PDB. This has the benefit that it will load additional
metadata provided by the source, such as annotations and cross references. I will read from PFAM seed database. On the desktop, select File and from the drop
down menu, select Fetch Sequences. This open up a New Sequence Fetcher window,
press database button, to open the window listing all the databases that Jalview can
access. Scroll down this and select the PFAM seed
database. Return to New Sequence Fetcher window and enter the id PF03460, and click OK. Jalview will now load this alignment directly from PFAM database. Next I will read a sequence data from the
Uniprot database. Again select File and in the drop down menu,
select Fetch Sequences, press the database selection button to open
the new database window, and select Uniprot option. Enter the id number P00340 in the New Sequence
Fetcher window, and click OK to retrieve the sequence data. NOTE: Several sequences can be loaded at the
same time by using semicolons to separate each of the ids. Jalview can read sequence directly from a
URL by dragging and dropping the url from the address panel of your web browser on to
the Jalview desktop. If you have a problem it might help changing
browser. Alternatively you can go to file and in the
drop down menu select Input Alignment, and from there select from URL.
Enter the URL and click ok. And this will read in the sequences. If you want to see our other Jalview training
video, then please visit our web site at www.jalview.org Good bye.

2 Replies to “Loading protein sequences and alignments into Jalview”

  1. Great resource video, using Jalview for 1st time, very clear narration, helping me get started. I'm familiar with many multiple sequence alignment tools online, but I usually use Adobe Illustrator or CorelDraw (a very old version) to manually colour residues of interest. This will save time I hope!

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