<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>
EMBOSS 1.6.0 has now been released.
<p>Two new applications:
<p> (1) cons - calculates a consensus sequence from a multiple
sequence alignment. To obtain the consensus, the sequence weights and a
scoring matrix are used to calculate a score at each position in the alignment.
<br> The "plurality" option allows the user to set a cut-off
for the number of positive matches below which there is no consensus.
<br> The "identity" option provides the facility of setting
the required number of identities at a site for it to give a consensus
at that position. Therefore, if this is set to the number of sequences
in the alignment only columns of identities contribute to the consensus.
<br> The "setcase" option sets the threshold for the
positive matches above which the consensus is is upper-case and below which
the consensus is in lower-case.
<p>(2) plotcon - displays a graphical representation of the similarity
along a set of aligned sequences.
<p>The similarity is calculated by moving a window of a specified length
along the aligned sequences. Within the window, the similarity of any one
position is taken to be the average of all the possible pairwise scores
of the bases or residues at that position. The pairwise scores are taken
from the specified similarity matrix. The average of the position similarities
within the window is plotted. The program may be useful is determining
where the quality of alignments are good or bad.
<br>
<p>Tim
<pre>--
Tim Carver, PhD,
Bioinformatics, MRC HGMP Resource Centre,
Hinxton, Cambridge, CB10 1SB
</pre>
</html>