LePA Proteins is a learning tool that shows us all the intermediate steps and partial results of a pair-wise alignment of aminoacid sequences.
DIRECTIONS OF USE:
First of all, we have to introduce the two aminoacid sequences in the textfields (only the 20 aminoacid characters).
Then we choose one of the three methods available:
- Global: this is the 'normal' method.
- Semiglobal: when one sequence is much longer than the other and we do not give value to the gaps in order to get a more realistic punctuation.
- Local: when we want to find just the longest identical part of both sequences.
Next we have to put the desired values to the GAP field which will be used in the calculations. Pressing the 'Matching Matrix' button
we can see the matching values for all the aminoacids pairs in a new window.
To start we press the ALIGN button and we can see how two matrix appear in the visualization area. On the left side we have
the Scoring Matrix which shows the partial punctuations of the alignment. And on the right matrix we can see the possible alignments
until that moment.
There are four buttons:
- Diagonal: It shows the next step in the calculations, filling one diagonal of the matrixes.
- Complete: It finishes the calculations, showing all the values in the matrixes.
- Results: It shows the final alignments with their punctuations on the lower window and also on the second matrix with a red line.
- Repeat: To make a new alignment.