| topo

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

## 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 tsw:aqp1_human -signa -prol=UM -cys=cg -gly=sr -acid=dr -basic=db -ohaa=da -araa=dg -graph ps
    Draws an image of a transmembrane protein
    Transmembrane Sections: 18 35 49 67 94 115 136 156 165 184 211 232
    First membrane from the outside [Y]: n
    Signature Sections: 74 82 sy 189 189 hm 239 239 sa 157 157 sa 262 262 sa

    Created topo.ps

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Draws an image of a transmembrane protein
    Version: EMBOSS:6.2.0

       Standard (Mandatory) qualifiers (* if not always prompted):
      [-sequence]          sequence   Protein sequence filename and optional
                                      format, or reference (input USA)
       -sections           range      [(full sequence)] 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       boolean    [Y] First membrane from the outside
       -signature          toggle     [N] Are there any signature areas to be
                                      marked
    *  -sigrange           range      [(full sequence)] 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
       -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                      (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                      tek, tekt, none, data, xterm, png, gif)

       Additional (Optional) qualifiers:
       -cyssymbol          menu       [CF] Code representing shape and colour for
                                      cys
                                      i.e. SR square red, HY hexagon yellow
                                      CF circle NOfill, UG up arrow green (Values:
                                      N (None); CF (circle); SF (square); HF
                                      (hexagon); UF (up arrow); 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))
       -glysymbol          menu       [CF] Symbol to display N-glycosylation sites
                                      outside of membrane see cyssymbol for
                                      examples (Values: N (None); CF (circle); SF
                                      (square); HF (hexagon); UF (up arrow); 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))
       -acidicaa           menu       [CF] Symbol to display acidic amino acids
                                      (Values: N (None); CF (circle); SF (square);
                                      HF (hexagon); UF (up arrow); 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))
       -basicaa            menu       [CF] Symbol to display basic amino acids
                                      (Values: N (None); CF (circle); SF (square);
                                      HF (hexagon); UF (up arrow); 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))
       -amineaa            menu       [CF] Symbol to display amine amino acids
                                      (Values: N (None); CF (circle); SF (square);
                                      HF (hexagon); UF (up arrow); 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))
       -ohaa               menu       [CF] Symbol to display OH- amino acids
                                      (Values: N (None); CF (circle); SF (square);
                                      HF (hexagon); UF (up arrow); 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))
       -araa               menu       [CF] Symbol to display aromatic amino acids
                                      (Values: N (None); CF (circle); SF (square);
                                      HF (hexagon); UF (up arrow); 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))
       -proline            menu       [CF] Symbol to display prolines (Values: N
                                      (None); CF (circle); SF (square); HF
                                      (hexagon); UF (up arrow); 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))
       -draft              boolean    [N] Is this a draft plot

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of the sequence to be used
       -send1              integer    End of the sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-graph" associated qualifiers
       -gprompt            boolean    Graph prompting
       -gdesc              string     Graph description
       -gtitle             string     Graph title
       -gsubtitle          string     Graph subtitle
       -gxtitle            string     Graph x axis title
       -gytitle            string     Graph y axis title
       -goutfile           string     Output file for non interactive displays
       -gdirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | sequence | Protein sequence filename and optional format, or reference (input USA) | Readable sequence | Required
-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 | Sequence range | full sequence
-[no]membrane | boolean | First membrane from the outside | Boolean value Yes/No | Yes
-signature | toggle | Are there any signature areas to be marked | Toggle value Yes/No | No
-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 | Sequence range | full sequence
-graph | graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (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

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display N-glycosylation sites outside of membrane see cyssymbol for examples

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display acidic amino acids

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display basic amino acids

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display amine amino acids

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display OH- amino acids

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display aromatic amino acids

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

list

Symbol to display prolines

N | (None)
CF | (circle)
SF | (square)
HF | (hexagon)
UF | (up arrow)
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

-draft | boolean | Is this a draft plot | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1 -sbegin_sequence | integer | Start of the sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-graph" associated graph qualifiers
-gprompt | boolean | Graph prompting | Boolean value Yes/No | N
-gdesc | string | Graph description | Any string | Membrane topology
-gtitle | string | Graph title | Any string |
-gsubtitle | string | Graph subtitle | Any string |
-gxtitle | string | Graph x axis title | Any string |
-gytitle | string | Graph y axis title | Any string |
-goutfile | string | Output file for non interactive displays | Any string |
-gdirectory | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

Any sequence.

### Input files for usage example

'tsw:aqp1_human' is a sequence entry in the example protein database 'tsw'

### Database entry: tsw:aqp1_human

    ID   AQP1_HUMAN              Reviewed;         269 AA.
    AC   P29972; Q8TBI5; Q8TDC1;
    DT   01-APR-1993, integrated into UniProtKB/Swiss-Prot.
    DT   23-JAN-2007, sequence version 3.
    DT   16-JUN-2009, entry version 108.
    DE   RecName: Full=Aquaporin-1;
    DE            Short=AQP-1;
    DE   AltName: Full=Aquaporin-CHIP;
    DE   AltName: Full=Water channel protein for red blood cells and kidney proximal tubule;
    DE   AltName: Full=Urine water channel;
    GN   Name=AQP1; Synonyms=CHIP28;
    OS   Homo sapiens (Human).
    OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
    OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
    OC   Catarrhini; Hominidae; Homo.
    OX   NCBI_TaxID=9606;
    RN   [1]
    RP   NUCLEOTIDE SEQUENCE [MRNA], AND PARTIAL PROTEIN SEQUENCE.
    RX   MEDLINE=92107900; PubMed=1722319; DOI=10.1073/pnas.88.24.11110;
    RA   Preston G.M., Agre P.;
    RT   "Isolation of the cDNA for erythrocyte integral membrane protein of 28
    RT   kilodaltons: member of an ancient channel family.";
    RL   Proc. Natl. Acad. Sci. U.S.A. 88:11110-11114(1991).
    RN   [2]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    RX   MEDLINE=93340184; PubMed=8340403;
    RA   Moon C., Preston G.M., Griffin C.A., Jabs E.W., Agre P.;
    RT   "The human aquaporin-CHIP gene. Structure, organization, and
    RT   chromosomal localization.";
    RL   J. Biol. Chem. 268:15772-15778(1993).
    RN   [3]
    RP   NUCLEOTIDE SEQUENCE [MRNA].
    RC   TISSUE=Retinal pigment epithelium;
    RX   MEDLINE=96326579; PubMed=8703970; DOI=10.1016/0005-2736(96)00076-4;
    RA   Ruiz A.C., Bok D.;
    RT   "Characterization of the 3' UTR sequence encoded by the AQP-1 gene in
    RT   human retinal pigment epithelium.";
    RL   Biochim. Biophys. Acta 1282:174-178(1996).
    RN   [4]
    RP   NUCLEOTIDE SEQUENCE [MRNA].
    RC   TISSUE=Uterus;
    RX   MEDLINE=94290349; PubMed=7517253;
    RA   Li X., Yu H., Koide S.S.;
    RT   "The water channel gene in human uterus.";
    RL   Biochem. Mol. Biol. Int. 32:371-377(1994).
    RN   [5]
    RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANTS VAL-45 AND ASP-165.
    RG   SeattleSNPs variation discovery resource;
    RL   Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
    RN   [6]

      [Part of this file has been deleted for brevity]

    FT   TRANSMEM    137    155       Helix 4.
    FT   TOPO_DOM    156    166       Cytoplasmic.
    FT   TRANSMEM    167    183       Helix 5.
    FT   TOPO_DOM    184    186       Extracellular.
    FT   TOPO_DOM    187    192       In membrane.
    FT   TRANSMEM    193    200       Helix E.
    FT   TOPO_DOM    201    207       Extracellular.
    FT   TRANSMEM    208    228       Helix 6.
    FT   TOPO_DOM    229    269       Cytoplasmic.
    FT   MOTIF        76     78       NPA 1.
    FT   MOTIF       192    194       NPA 2.
    FT   COMPBIAS    159    162       Poly-Arg.
    FT   SITE         56     56       Substrate discrimination.
    FT   SITE        180    180       Substrate discrimination.
    FT   SITE        189    189       Hg(2+)-sensitive residue.
    FT   SITE        195    195       Substrate discrimination.
    FT   MOD_RES     246    246       Phosphothreonine (By similarity).
    FT   MOD_RES     247    247       Phosphoserine (By similarity).
    FT   MOD_RES     262    262       Phosphoserine.
    FT   CARBOHYD     42     42       N-linked (GlcNAc...).
    FT   CARBOHYD    205    205       N-linked (GlcNAc...) (Potential).
    FT   VARIANT      38     38       P -> L (in Co(A-B-) antigen; non
    FT                                functional AQP1; red cells show low
    FT                                osmotic water permeability).
    FT                                /FTId=VAR_013279.
    FT   VARIANT      45     45       A -> V (in Co(A-B+) antigen;
    FT                                dbSNP:rs28362692).
    FT                                /FTId=VAR_004400.
    FT   VARIANT     165    165       G -> D (in dbSNP:rs28362731).
    FT                                /FTId=VAR_022318.
    FT   CONFLICT     45     45       A -> T (in Ref. 7; AAH22486).
    FT   HELIX         8     35
    FT   STRAND       37     42
    FT   HELIX        48     65
    FT   STRAND       68     71
    FT   HELIX        76     83
    FT   HELIX        94    114
    FT   TURN        119    122
    FT   STRAND      132    135
    FT   HELIX       136    154
    FT   HELIX       166    182
    FT   TURN        183    185
    FT   HELIX       192    199
    FT   HELIX       207    227
    SQ   SEQUENCE   269 AA;  28526 MW;  BA204D82FB26352E CRC64;
         MASEFKKKLF WRAVVAEFLA TTLFVFISIG SALGFKYPVG NNQTAVQDNV KVSLAFGLSI
         ATLAQSVGHI SGAHLNPAVT LGLLLSCQIS IFRALMYIIA QCVGAIVATA ILSGITSSLT
         GNSLGRNDLA DGVNSGQGLG IEIIGTLQLV LCVLATTDRR RRDLGGSAPL AIGLSVALGH
         LLAIDYTGCG INPARSFGSA VITHNFSNHW IFWVGPFIGG ALAVLIYDFI LAPRSSDLTD
         RVKVWTSGQV EEYDLDADDI NSRVEMKPK
    //

## Output file format

### Output files for usage example

### Graphics File: topo.ps

## 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

Program name | Description
--- | ---
garnier | Predicts protein secondary structure using GOR method
helixturnhelix | Identify nucleic acid-binding motifs in protein sequences
hmoment | Calculate and plot hydrophobic moment for protein sequence(s)
pepcoil | Predicts coiled coil regions in protein sequences
pepnet | Draw a helical net for a protein sequence
pepwheel | Draw a helical wheel diagram for a protein sequence
tmap | Predict and plot transmembrane segments in protein sequences

## Author(s)

This program is an EMBOSS conversion of a Fortran program 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.

Changes to the functionality in version 2 have been ported to the EMBOSS version.

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None