


1) MotifMaker
--------------
In this example, the proteins from APE family are analyzed for conserved
motifs. The input file for this task is a multiple sequence alignment
(ape-alignment.aln) and parameters. Run "motifmaker -?" for a brief
description.  The apes are stored in the directory 01-ape-mmaker. (Note
that the ending "/".) See the generated .html file for output.

motifmaker -a ape-alignment.aln -v 0,1,0.1 -g 2 -l 4 -t signif -p 01-ape-mmaker/


2) MotifSearch I
----------------
Now, search the protein database or sequences which contain motifs identified
in the previous step. The input files are:
- multiple sequence alignment (ape-alignment.aln)   .. this is necessary to gather statistics
- the protein database (ASTRAL40v1.55.txt)
- a profile describing the multiple sequence alignment (*.gprf)
- the motif definitions (*.prf)

motifsearch -a ape-alignment.aln -d ASTRAL40v1.55.txt -g 01-ape-mmaker/01-ape-mmaker.gprf -m 01-ape-mmaker/01-ape-mmaker.prf -p 02-ape-msearch/



3) MotifSearch II
-----------------
One can also search in the protein database for a profile substring. The input
files are: 
- multiple sequence alignment (ape-alignment.aln)
- the protein database (ASTRAL40v1.55.txt)
- a profile describing the multiple sequence alignment (*.gprf)
- the motif definitions (*.prf)     .. this still required, because -s can be used in combination with the -M option.
- the profile substring, based on the reference sequence (YTFWTYMMN)

motifsearch -d ASTRAL40v1.55.txt -p 03-ape-msearch/ -a ape-alignment.aln -s YTFWTYMMN -g 01-ape-mmaker/01-ape-mmaker.gprf -m 01-ape-mmaker/01-ape-mmaker.prf -t 0.1 -M 5,6

NOTE: The substring YTFWTYMMN is returned with a very low score although the
first sequence (d1hd7a) contains a perfect match. This is to demonstrate that the
search is being done against the profile data (low relative entropies) and not 
against the string.


4) MotifSearch III
------------------
MotifSearch can be also used to search against an arbitrary string (with no
profile data). In this case, the input files are:
- a simplistic multiple sequence alignment (substring-search.txt), containing
  only the searched string. Admittedly, this is not very user-friendly and may
  be changed in the future.
- the protein database (ASTRAL40v1.55.txt)

motifsearch -d ASTRAL40v1.55.txt -s YTFWTYMMN -p 04-ape-msearch/ -a substring-search.txt

Note that the substring has a score of the perfect match for the string YTFWTYMMN.



4) MotifSearch IV 
-----------------
To see what are the scores for each position of a sequence, MotifSearch can be run
in a detailed display mode. The input files are:
- the database to run detailed scores on (for-msearch-detailed.txt) .. run only
  for few sequences, not for the whole Astral database!
- a profile describing the multiple sequence alignment (*.gprf)
- the motif definitions (*.prf)

motifsearch -d for-msearch-detailed.txt -D -p 05-ape-msearch/ -s YTFWTYMMN -g 01-ape-mmaker/01-ape-mmaker.gprf -m 01-ape-mmaker/01-ape-mmaker.prf -M 5,6
motifsearch -d for-msearch-detailed.txt -D -p 05-ape-msearch/ -s YTFWTYMMN (detailed scores for an arbitrary substring)



5) MotifMaker
-------------
Produce variability plot of the flavivirus envelope protein based on consensus sequences 
of 29 flaviviruses. The input files are:
- the alignment (flavi-alignment.aln)

motifmaker -a flavi-alignment.aln -v 0,1,0.1 -g 2 -l 4 -t signif -p 06-flavi-motifmaker/



6) Variability plot (entropies)
-------------------------------
Produce variability plot of the flavivirus envelope protein based on consensus sequences 
of 29 flaviviruses. The input files are:
- the alignment (flavi-alignment.aln)
- the PDB file (1oan.pdb)

variability-plot -a flavi-alignment.aln -P 1oan.pdb -c A -p 07-flavi-variability/ -i DV2 -e



7) Variability plot (motifs)
---------------------------
Map the motifs created by MotifMaker on a PDB structure. The input files are:
- the alignment used by MotifMaker to generate the motifs (flavi-alignment.aln)
- the motifs (*.prf)
- the PDB file (1oan.pdb)

variability-plot -a flavi-alignment.aln -P 1oan.pdb -c A -p 08-flavi-motifs/ -i DV2 -M 06-flavi-motifmaker/06-flavi-motifmaker.prf



For more information, please see the PCPMer website. 




