Jemboss Alignment Viewer

This is under development at the HGMP-RC. Let us know what features you would like to see this viewer software provide.

Loading Sequences

Supported sequence file formats are FASTA and MSF (so far). Load the aligned sequences in via the "File" menu and "Open".

When loaded the alignment appears in the order the sequences appear in the sequence file. The name is on the right hand side with the length of each sequence. At the top of the editor is the relative sequence numbering. A tooltip popup when the mouse arrow is placed over a site. The tooltip gives the name of the sequence, the residue and the position of that site.

Editing Functions

Gaps can be introduced into a sequence by clicking on a site and dragging the mouse to the right. Gaps can similarly be removed by dragging to the left. Sequences can be deleted from the the viewer by right mouse clicking on the sequence and selecting "Delete" from the pop up menu.

Sequences can be locked by selecting the name on the right hand side of the alignment and clicking the 'Lock' button. When gaps are then introduced into one of these sequences the gap will also appear in those sequence in this group of locked sequences. The lock can be switched off with the 'Unlock' button or 'Unlock All Sequences' in the 'Edit' menu.

Also under the 'Edit' menu there is an utility to trim the ends of sequences. This can be used to tidy up the termini of an alignment.

Colour Schemes

There are various colour schemes for the residues these can be found under the View menu. The residues can be coloured by there property or using one of the other common colour schemes (e.g. the Taylor method). These colour schemes can be edited using the "Colour Display" window and right clicking on a colour to bring up a palette to select from.

Alternatively sequences can be coloured based on their identities and their positive matches. The positive matches are defined by the scoring matrix selected. This method is based on the EMBOSS program prettyplot colour scheme.

Scoring Matrix

The are used to calculate scores in the consensus. A different scoring matrix can be selected from the "View" menu and clicking on "Matrix Display". The current scoring matrix being used is reported at the bottom of the alignment viewer.

Consensus Sequence

This uses the same algorithm as used by cons in EMBOSS. The consensus when calculated appears below the other sequences in the viewer.

Consensus Plot

Gives a graphical representation of the consensus. This is based on plotcon in EMBOSS.

Identity Table

This can be calculated and gives the percentage of identical matches between each pair of sequences.

W.R.Taylor Protein residue colour references: Protein Eng. vol.10 no. 7 pp743-746, 1997


tcarver@hgmp.mrc.ac.uk