Can I use formats other than CLUSTALW (.ALN) for input ?
Unfortunately at this time NO. In the future versions we will
allow to add multiple alignments in .PRF format. Also user will
be able to input structural alignments in DALI or CE formats.
Will this program work with nucleic acid sequence ?
No. This program can work only with proteins. Simple script to
convert your genome into protein (six frame) can be written which
can then be used for flagging motifs from genomes.
Does this program has a built-in motif library ?
Currently no. In the future we may have standard functional motifs for
protein families.
Can this program calculate RMSD if I have structures available ?
No. The program does not do it currently. In the future we may provide
the option to the user.
I have a non-standard amino acid. Will this program work ?
No. It will raise an error if it encounters any non-standard amino acids.
How can I make this program run on a PC-DOS ?
We have tested PCPMer on PC-DOS. The user must install active perl. And
manually do certain modifications. Interested users can contact venkat@bohr.utmb.edu
for further directions.
Does my sequence database need to be in any specific format ?
Yes. It should be in FASTA format, with name of the sequence indicated by >.
No two sequence can have identical names.
Can the program optimize input parameters (R,G,L) automatically ?
Although we have subroutines built-in to do it, we haven't emphasized this
in our manual. Advanced user can user can read the technical manual for the
optimize routines.
I want to shuffle the motifs or restrict the order of motif occurrence. How will I do it ?
The future version will have such functionality. Currently the program assumes motif occurrence
to be independent of the position. Advanced users can write their own script to filter using
.PCPscore as the data file. Residue position of motif occurrence is available in that file.
I have one big motif for the entire protein family. What should I do ?
You need to increase your R cutoff or include more diverse members in the multiple
alignment.
I have too many small motifs. What should I do ?
Decrease R value. Increase L-cutoff.
My protein family has 100% conserved sequence. Can I use this program ?
No.
How important is the multiple alignment ?
It is the most critical in obtaining correct result. You need to include more
diverse sequence and should avoid adding identical sequences to prevent weighting
bias.
This version can do the following:
Identify motifs and created corresponding PCP profiles automatically in a protein family
Score a motif profile against a sequence and list the highest scoring windows
Scores a database of protein sequences and sorts highest scoring sequence that may be related to a protein family.
Where can I download the New quantitive descriptors?
