Loading Sequences

Sequences may be retrieved from public databases or loaded from a file.

  1. Launch Jalview and/or select Window $\Rightarrow$ Close All in the desktop window to close all windows.

  2. Loading sequences from Public Database: Select File $\Rightarrow$ Fetch Sequences… from the desktop menu. Click on the tab –Select Database– in the New Sequence Fetcher dialog box and select the PFAM (Seed) database. Enter the accession number PF03460 and click OK. An alignment of about 170 sequences should load.

  3. Loading sequences from URL: Selecting File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL from the desktop menu, enter https://www.jalview.org/tutorial/alignment.fa in the dialog box and click OK.

  4. Save the fasta file (.fa) onto your computer using File $\Rightarrow$ Save as in the alignment menu, and save the file in an appropriate folder.

  5. Loading sequences from a file: Open the file you have just saved on your computer by selecting File $\Rightarrow$ Input Alignment $\Rightarrow$ From File, select the file that you saved, and click Open.

  6. Loading sequences by ‘Drag and Drop’: Drag the fasta file that you saved from its folder and drop it onto the Jalview desktop window, the alignment opens in a new alignment window. Repeat this process but drop the file on a Jalview alignment window, this adds the sequences below the other sequences in the alignment.

For more information on this topic go to section 1.4 of the Jalview manual.
 This exercise can be viewed in the Loading protein sequences and alignments video.