EMBOSS: topo

| ## EMBOSS: topo

# Program topo

## Function

TOPO creates an image of a transmembrane protein.

## Description

TOPO creates an image of a transmembrane region but the user must give the transmembrane regions for the sequence as it does not calculate these.

## Usage

Here is a sample session with topo.

    % topo sw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr
    -basic=db -ohaa=da -araa=dg

    Draws an image of a transmembrane protein
    Display on device [xwin]:
    Transmembrane Sections: 18 35 49 67 94 115 136 156 165 184 211 232
    First membrane from the outside [Y]: n
    Signatue Sections: 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa

click here for result

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-sequence]          sequence   Sequence USA
       -graph              graph      Graph type
       -sections           range      Examples of region specifications are:
                                      24-45, 56-78
                                      1:45, 67=99;765..888
                                      1,5,8,10,23,45,57,99
       -[no]membrane       bool       First membrane from the outside
    *  -sigrange           range      Examples of ranges specifications are:
                                      10-10 CF, 56-78 SY\ 1:45 SR, 67=99
                                      HY;765..888 SF
                                      1,5,HG,8,10,HY,23,45,SR,57,99,UG

       Optional qualifiers:
       -cyssymbol          list       Code representing shape and colour for cys
                                      i.e. SR square red, HY hexagon yellow
                                      CF circle NOfill, UG up arrow green
       -glysymbol          list       Symbol to display N-glycosylation sites
                                      outside of membrane see cyssymbol for
                                      examples
       -acidicaa           list       Symbol to display acidic amino acids
       -basicaa            list       Symbol to display basic amino acids
       -amineaa            list       Symbol to display amine amino acids
       -ohaa               list       Symbol to display OH- amino acids
       -araa               list       Symbol to display aromatic amino acids
       -proline            list       Symbol to display prolines
       -signature          bool       Are there any signature areas to be marked
       -draft              bool       Is this a draft plot

       Advanced qualifiers: (none)

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence USA | Readable sequence | Required
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm | EMBOSS_GRAPHICS value, or x11
-sections | Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 | Sequence range | full sequence
-[no]membrane | First membrane from the outside | Yes/No | Yes
-sigrange | Examples of ranges specifications are: 10-10 CF, 56-78 SY\ 1:45 SR, 67=99 HY;765..888 SF 1,5,HG,8,10,HY,23,45,SR,57,99,UG | Sequence range | full sequence
Optional qualifiers | Allowed values | Default
-cyssymbol | Code representing shape and colour for cys i.e. SR square red, HY hexagon yellow CF circle NOfill, UG up arrow green |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-glysymbol | Symbol to display N-glycosylation sites outside of membrane see cyssymbol for examples |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-acidicaa | Symbol to display acidic amino acids |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-basicaa | Symbol to display basic amino acids |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-amineaa | Symbol to display amine amino acids |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-ohaa | Symbol to display OH- amino acids |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-araa | Symbol to display aromatic amino acids |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-proline | Symbol to display prolines |
N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrpw)
DF | (down arrow)
C | (black circle)
CG | (green circle)
CR | (red circle)
CB | (blue circle)
CA | (aqua circle)
CM | (magenta circle)
CY | (yellow circle)
S | (black square)
SG | (green square)
SR | (red square)
SB | (blue square)
SA | (aqua square)
SM | (magenta square)
SY | (yellow square)
H | (black hexagon)
HG | (green hexagon)
HR | (red hexagon)
HB | (blue hexagon)
HA | (aqua hexagon)
HM | (magenta hexagon)
HY | (yellow hexagon)
U | (black up arrow)
UG | (green up arrow)
UR | (red up arrow)
UB | (blue up arrow)
UA | (aqua up arrow)
UM | (magenta up arrow)
UY | (yellow up arrow)
D | (black down arrow)
DG | (green down arrow)
DR | (red down arrow)
DB | (blue down arrow)
DA | (aqua down arrow)
DM | (magenta down arrow)
DY | (yellow down arrow)
| CF
-signature | Are there any signature areas to be marked | Yes/No | No
-draft | Is this a draft plot | Yes/No | No
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any sequence.

## Output file format

## Data files

## Notes

As you can see the lists above the are alot of options to choose for the displays of acidic, basic amino acids etc. This can be explained simply as :-

One letter codes are black filled shaped EXCEPT for "N" which means NONE (no shape).

For two letter codes the first letter is the shape and the second the colour except for "F" which means NO FILL.

For the signatures you need to input sets of start position, end position and code. For the example given these are 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa

    So residues 74 to 82 will have Yellow Squares (sy).
       residue 189 (i.e. 189 to 189) will have a Magenta Hexagon. (hm)

## References

## Warnings

## Diagnostics

## Exit status

## Known bugs

## See also

## Author(s)

The original Fortran program was written by Susan Jean Johns, VADMS Center, Biochemistry/Biophysics Department at WSU.

This application was modified for inclusion in EMBOSS by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## Priority

## Target users

## Comments