EMBOSS at CSC

Tehdyt toimenpiteet

EMBOSS: topo

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:6.3.0

   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, pdf,
                                  svg, pdf, svg)

   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

-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, pdf, svg, pdf, svg

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)

-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)

-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)

-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)

-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)

-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)

-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)

-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)

-draft

boolean

Is this a draft plot

Boolean value Yes/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

-send1
-send_sequence

integer

End of the sequence to be used

Any integer value

-sreverse1
-sreverse_sequence

boolean

Reverse (if DNA)

Boolean value Yes/No

-sask1
-sask_sequence

boolean

Ask for begin/end/reverse

Boolean value Yes/No

-snucleotide1
-snucleotide_sequence

boolean

Sequence is nucleotide

Boolean value Yes/No

-sprotein1
-sprotein_sequence

boolean

Sequence is protein

Boolean value Yes/No

-slower1
-slower_sequence

boolean

Make lower case

Boolean value Yes/No

-supper1
-supper_sequence

boolean

Make upper case

Boolean value Yes/No

-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

-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

-stdout

boolean

Write first file to standard output

Boolean value Yes/No

-filter

boolean

Read first file from standard input, write first file to standard output

Boolean value Yes/No

-options

boolean

Prompt for standard and additional values

Boolean value Yes/No

-debug

boolean

Write debug output to program.dbg

Boolean value Yes/No

-verbose

boolean

Report some/full command line options

Boolean value Yes/No

-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

-warning

boolean

Report warnings

Boolean value Yes/No

-error

boolean

Report errors

Boolean value Yes/No

-fatal

boolean

Report fatal errors

Boolean value Yes/No

-die

boolean

Report dying program messages

Boolean value Yes/No

-version

boolean

Report version number and exit

Boolean value Yes/No

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; B5BU39; Q8TBI5; Q8TDC1;
DT   01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   15-JUN-2010, entry version 123.
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       Helical; Name=Helix 4.
FT   TOPO_DOM    156    166       Cytoplasmic.
FT   TRANSMEM    167    183       Helical; Name=Helix 5.
FT   TOPO_DOM    184    186       Extracellular.
FT   INTRAMEM    187    192
FT   INTRAMEM    193    200       Helical; Name=Helix E.
FT   TOPO_DOM    201    207       Extracellular.
FT   TRANSMEM    208    228       Helical; Name=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. 9; 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

[topo results]

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

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 formerly at:
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

CSC

Tehdyt toimenpiteet

Wiki

Function

Description

Usage

Command line arguments

Input file format

Input files for usage example

Database entry: tsw:aqp1_human

Output file format

Output files for usage example

Graphics File: topo.ps

Data files

Notes

References

Warnings

Diagnostics

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments