[ssml] Retrieval of sequences listed in a publication / Visualization and Comparison of consensus Sequences

[Georg Fuellen]

Dear Collegues,

This is a short announcement regarding two tools that you may find useful.

1) paper2sequences: Retrieval of sequences listed in a publication

Imagine you're reviewing a paper that discusses some alignment of sequences,
and you want to reconstruct the alignment yourself...
Imagine you want to create a profile or HMM for a search for additional
homologs of some protein family discussed in a paper...

And imagine that you do not want to go through the hassle
of retrieving all the sequences by yourself, one by one. Then,
it may be worth using paper2sequences to retrieve the sequences all
in one go, by copy-pasting the usual "Table 1" of protein identifiers, names,
amino acid lengths, etc, from the PDF or HTML version of the paper, at

http://bibiserv.techfak.uni-bielefeld.de/paper2seq/

Feedback is welcome to Henning Mersch, hmersch at techfak.uni-bielefeld.de

2) VisCoSe: Visualization and Comparison of consensus Sequences

Now that you have the alignment (see above), imagine you want to
visualize motifs that are significant for certain subsets of the sequences,
motifs they have in common or motifs that distinguish them.
Then, VisCoSe is what you need:

http://viscose.ifg.uni-muenster.de/

Additionally, VisCoSe calculates histogram visualizations of
consensus sequences and conservation rates, and chemical properties
of the amino acids can be highlighted.

Feedback is welcome to Michael Spitzer, michael.spitzer at uni-muenster.de

--
best wishes,
Dr Georg Fuellen
integrated functional genomics, IZKF, medical faculty, university of muenster,
fuellen at alum.mit.edu - alum.mit.edu/www/fuellen/ - fax 49 251835 5651 - fon 2212