EMBOSS 1.6.0

[Tim Carver]

EMBOSS 1.6.0 has now been released.

Two new applications:

 (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.
   The "plurality" option allows the user to set a cut-off for the
number of positive matches below which there is no consensus.
    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.
    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.

(2) plotcon - displays a graphical representation of the similarity
along a set of aligned sequences.

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.


Tim

--
Tim Carver, PhD,
Bioinformatics, MRC HGMP Resource Centre,
Hinxton, Cambridge, CB10 1SB


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.open-bio.org/pipermail/emboss/attachments/20001006/c3be9d1e/attachment-0001.html>