from
an aligned multiple sequence file
Introduction:
If a multiple-sequence alignment is available
(.msf file generated by the GCG program), VHMPT can calculate the conservation
score for each aligned amino acid. In the display, the conservation score
is color-coded, with increasing red representing a higher degree of conservation
and increasing blue a higher degree of variation. This allows users
to identify, for example, highly conserved regions on the schematically
represented 2D topology of the membrane protein. The calculated scores
can be saved in a .score file which can then be opened directly next time
around.
Instructions:
-
Step 1:
-
choose File/Open/.msf & .helixseq
file and you can see a dialog box (Fig. 4) open.
Fig. 4 |
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Step 2:
-
Enter the .msf file name (the multiple sequence alignment
file generated by GCG) and the reference protein name (you can browse them
with the "Browse ..." button after the .msf file has been entered). Enter
a file name to which VHMPT can save the calculated amino acid conservation
scores. Then provide the amino acid sequence range of each transmembrane
(TM) helix in the protein. You can input these helices' beginning and ending
sequence numbers with a file (See Fig. 5a) or type them manually (Fig.
5b). (For manual input, the maximal number of helices is currently set
to 30.) For a detail description of the files .msf,
.helixseq, and .score,
see Appendix C, A, D.
Fig. 5a |
Fig. 5b |
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Step 3:
-
Choose OK, and you can see VHMPT draw the topology
of the protein.
Fig. 6 |