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
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.