| Help for MIP-based Sequence Identification | Close Window |
This program enables a user to identify Legionella species based on the sequence of the mip gene. Initially the 5 closest sequences are retrieved from a BLAST database of 155 confirmed Legionella mip sequences. These sequences are aligned along with the user sequence with a reference alignment containing representative species that span the whole breadth of the Legionella genus.
We recommend that you analyse a sequence in the following order:
First specify the mip sequence that you would like to use for identification by uploading a file using the browse button: 
and specifying the format of this sequence file using the drop-down menu
. Most common sequence types can be specified. Alternatively paste raw sequence into the box and give the sequence a simple name without punctuation.
Pressing each of the buttons below will start this alignment. Be warned this may take a while!
Click on this button to display an alignment of all the sequences from the reference alignment, top 5 database matches and the user sequence. The percentage indentities for each of these sequence will also be displayed. If the 3 closest database matches are included they will be coloued in green and the user sequence in red.
Click on this button to display a neighbour-joining tree of the alignment. This will include the reference species, the 5 closest matches from the database (coloured in green), and the user sequence (coloured in red).
Click on this button to display an alignment of the 8 sequences from the combined reference alignment that are most similar to the user sequence. Colours are as above.
If you have any feedback or queries please contact Anthony Underwood.
