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POSA: Partial Order Structure Alignment
POA: Partial Order Alignment
POG: Partial Order Graph
POSA was developed to generate partial order alignments, which means
that the output alignments are partial order graphs. So NO alignments
in the typical column-row format will be provided.
POSA server provides two ways for displaying the partial order
alignments; one can browse the alignment through our
iterative webpage,
or download the alignment text file.
POSA generates partial order alignments, which means we cannot provide the typical column-row alignments in whatever formats.
Instead we provide TWO kinds of alignment output that might be useful for some users.
Here we use the POSA result of 3 calmodulin-like proteins to demonstrate. This page provides links to the two alignment outputs shown below.
(1) Partial Order Graph (POG) along with amino acids
This file (show me the demonstration file)
records the list of proteins between ...: d1ncx__ (index = 0), d2sas__ (index = 1) and d1jfja_ (index = 2).
Between and , each line represents
a node in the POG, recording residues aligned at this node. For examples,
"0 0 0 A" records node 0 (note: all indexes are from 0), meaning residue 0 (residues are indexed starting from 0 regardless the original index in the PDB file)
of protein 0 (i.e., d1ncx__), whose amino acid is A;
"20 0 20 E 2 0 M 1 8 K" records node 20, which represents an aligned position
common to all 3 input structures (i.e., protein 0 residue 20 E, protein 2 residue 0 M and protein 1 residue 8 K are aligned at this node).
Between and , each line records an edge connecting two nodes; e.g., "0 0 1" records edge 0 connecting node 0 and node 1.
Users may prepare alignments they desire by extracting alignment information from this file.
(2) Alignment of amino acids
This file (show me the demonstration file)
only explicitly lists the residues of aligned regions of at least 5-residues long shared by all input structures (but not
aligned positions of a subset of the input structures), while only shows the lengths of the other spanning regions between {}.
In the file, the first line shows that there are 6 such aligned regions, labeled as S1 - S6 (same as in
the simplified POSA graph).
The second line "d1ncx__ {20}EFKAAFDM{0}FDADGGGDIST{1}.." shows residues 21-28 of 1ncx__ (EFKAAFDM), 29-39 (FDADGGGDIST) and so on.
Partial order alignments from POSA can be visualized iteratively on our website. Currently
POSA supports two methods of displaying protein structures,
Chime and
Jmol.
You may choose your favorite method in the POSA submission page (default Jmol).
You need to have browser powered by Chime plugin to visualize the POSA output in Chime, while you
need to have browser that is powered by Java Applet and supports Javascript and Java Applet
communications to use Jmol.
Note: If you switch from Jmol to Chime or vice versa for a completed job,
you may get a messed up webpage. Reload your webpage may help.
Browsers that work for POSA:
Windows users: Probably all kinds of Browsers work in both ways, Chime and Jmol; of course after you have Chime plugin and JRE installed.
Linux users: many browsers (my favorite Mozilla) work for POSA in Jmol and Chime model,
though you need some tricks to install Chime plugin in
linux (ref).
Mac users: There is no chime plugin for Mac OSX. You may install Chime plugin in Mac classic mode in
netscape, which works but does not work well (I\'d rather not use it). New version of firefox (1.5v)
(mozilla) works for POSA using Jmol, but not older versions (like firefox 1.0). Safari does not work properly!
POSA server accepts structures (in PDB format) packed in either a tar (gzipped or not) or a zip file.
Be sure to only pack (a) clean PDB files
(e.g., use a filtered PDB file that only contains a specific chain you want to use, instead of the original PDB file
with multiple chains);
and (b) files in current directory (instead of files in a subdirectory or
mixed).
E.g., you have three structures, AAAA.pdb, BBBB.pdb and CCCC.pdb in current directory; you can archive these pdbs in three ways that
POSA server can recognize.
> tar cvf pdb.tar AAAA.pdb BBBB.pdb CCCC.pdb
> tar zcvf pdb.tar.gz AAAA.pdb BBBB.pdb CCCC.pdb
> zip pdb.zip AAAA.pdb BBBB.pdb CCCC.pdb
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