HELP LePMA (Learning Progressive Multiple Alignment)

    LePMA is a learning tool that shows us all the intermediate steps and partial results of a progressive multiple alignment of DNA sequences, and also the resultant cluster of the alignment.

1. Interface
interface


2. LePMA function
    2.1. Firstly, we have to introduce the sequences in Fasta format* into the incoming data area and fill the GAP,MATCH and MISSMATCH fields.
           In order to obtain biological sense during the alignments, the next formula should be accomplished:
               MATCH > MISSMATCH > 2*GAP
    2.2. Then, proceed to the execution of the alignment's first step just clicking the "START" button. After first step is carried out, we obtain, on one hand, the Similarity Matrix* with all similarity scores between every pair of sequences introduced and, on the other hand, the sequences list which the guide tree* will start from during the alignment process.
           Pressing any value from the Similarity Matrix* we can see the Pair-wise Scoring Matrix* which the value is calculated from and we can open the application LePA to see step by step how to calculate this Pair-wise Scoring Matrix*.
           Pressing any sequence or cluster name from the guide tree* we can get the concrete sequence or cluster aligned (after first step, we can see the sequences introduced; after next steps we can see the resultant aligned clusters). After next steps we can also open the application LeCA pressing a button to see step by step how to get the clusters using the cluster alignment algorithm.
    2.3. Proceed to the next step of the alignment just clicking "NEXT" button and observe the guide tree* evolution and the new Similarity Matrices* appearance.
    2.4. Repeat step 2.3 until the alignment finished or get the resultant cluster directly clicking "FINISH" button.

Notes:
    a) From the second step, the only values we can press in order to see its calculation are the new scores obtained from the last step of the alignment; in this case, we'll see the aproximation formula we use.
    b) Pressing the root of the guide tree* after last step of the alignment we can obtain its final result (the resultant cluster of the alignment done).

    * All these terms are explained in 'Concepts' area.