Annotation rows in Jalview
Channel: Jalview & Dundee Resource Online Training
Date: 02/04/2020

In this video, we discuss the annotation rows that are located below the sequence alignment in the Jalview desktop. Jalview is a free-to-use sequence alignment and analysis visualisation software linking genomic variants in DNA, protein alignments and 3D structure (http://www.jalview.org/).

Annotations and features provide additional information that is overlaid onto the sequences and the alignment. When Jalview opens an alignment, the conservation, consensus and quality annotations are automatically calculated. They are displayed as quantitative histograms. These annotations are associated with the columns in the alignment, thus reflecting the properties of the alignment as a whole.

We have another video that discusses features on an alignment, the link is https://youtu.be/nLINw__nfDg.

Annotation can either be dynamic, where changes in the alignment or sequence result in the annotation being recalculate. Or static, where the annotations are unaffected by changes in the alignment. 

For large alignments, the annotation calculation may slow down the program. This can be turned off by going to the ‘calculate’ drop down menu and toggle the ‘autocalculate consensus’ option off. 

The conservation annotation is a numerical index that quantifies the conservation of the physicochemical properties for each column of the alignment. The consensus annotation reflects the percentage of different amino acids per column. The quality score is calculated from the Blosum 62 scores. The conservation and quality annotations are calculated for amino acids, but not for nucleotides.

Jalview is able to display 4 different types of annotation rows. Type 1 are annotation rows which relate to the alignment as a whole, such as those that open when Jalview is launched. Type 2 are annotation rows which relate to a selected group within the alignment. Type 3 are sequence associated annotation rows, these are linked to a specific sequence within the alignment. Type 4 are annotation rows that the user defines, these are manually created annotations.

Annotation rows can be hidden or deleted. Annotations can be exported and opened in Jalview.

The alignment used in this tutorial can be accessed using the URL http://www.jalview.org/tutorial/alignment.fa.

This exercise can be found in our User Manual, available to download from the Jalview website (http://www.jalview.org/about/documentation). Other Jalview training videos can be viewed in the training section of the website (http://www.jalview.org/training/Training-Videos).

Jalview can access a wide range of databases including PFAM, PDB, EMBL and UniProt. It can read a variety of file formats including FASTA, PFAM, MSF, Clustal, BLC, PIR, Stockholm.
Jalview collaborates with several groups to offer a broad range of sequence analysis tools including: 
• multiple sequence alignment using Clustal Omega, Muscle, MAFFT, ProbCons, T-COFFEES, ClustalW, MSA Prob and GLProb
• tree calculations and principal component analysis (PCA)
• consensus, conservation, and functional site analysis
• secondary structure and disorder predictions
• visualisation of 3D structure.

Jalview (http://www.jalview.org/) has been developed in Geoff Barton's group (https://www.compbio.dundee.ac.uk/) in the School of Life Sciences (https://www.lifesci.dundee.ac.uk/) at the University of Dundee with the funding support of the BBSRC and the Wellcome Trust. The team has also developed software JPRED (http://www.compbio.dundee.ac.uk/www-jpred) and JABAWS (http://www.compbio.dundee.ac.uk/jabaws).

This video was produced by Dr Suzanne Duce, School of Life Sciences, University of Dundee.