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The Jemboss Alignment Editor (JAE) has been designed to combine a flexible multiple sequence alignment view and edit facility
with an option to graphically lay out the final display for export to a printer or publishable document. The editor can be accessed at
the Jemboss Tools menu or by selecting the appropriate alignment file and following the open with
option on the right click menu. Currently the JAE can read in any alignment file in either fasta or MSF format.
Fasta Format
This is the default format in EMBOSS and any alignment created using emma will be represented in this way. It consists of a
single greater than (>) sign at the very start of the file followed by the sequence name and its description. This must not exceed
the length of the first line. The second line is the beginning of the sequence, and the computer will treat anything written on or after this
line as part of the sequence. Thus if the sequence description runs over, the addiotnal part will be added to your sequence and analysed
accordingly. So your alignment in fasta format will consist of each sequence under each other, separated by sequence descriptions with
each sequence interspersed by a dash (-) to indicate where the program has inserted gaps to represent insertions and deletions.
It is difficult to get a good idea of an alignment in this format without using an alignment editor.
MSF Format
Multiple Sequence File Format is commonly found as the output format for alignments run using web servers or the GCG suite. It consists of each
sequence aligned in a block one underneath the next with the first 60 residues (or bases) of that alignment, often annotated with a series of asterisks,
colons and dots to indicate varying degrees of similarity. This formatting is repeated in as many blocks as it takes for the entire alignment to be
displayed. The asterisks indicate complete conservation of identity within a position, the colons that at least two of the residues in a postion match exactly.
A dot indicates similarity within the position as defined by a non-negative matrix score. This file can be selected as output when creating an alignment
with emma.
The alignment may then be edited by dragging sequence residues to the right to create manual insertions. This process may be aided by colouring the
alignment. This can be done according to a variety of parameters, or customised to optimse the alignment display.
Calculation options include the ability to display an identity matrix indicating pairwise identites for each combinations of sequences within the alignment.
The consensus can be displayed and parameters set to optimise the calculation. A consensus plot offers a graphical oportunity to visualise the areas of
conservation within the alignment. Should knowledge of the alignment scoring matrix be required, these can be accessed from the JAE.
For that elusive motif region, the find pattern option enables an automatic search throughout the alignment for a consecutive series of residues.
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