topo

 

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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 
Draw 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

Draw an image of a transmembrane protein
Version: EMBOSS:6.6.0.0

   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)

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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, 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)
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
-scircular1
-scircular_sequence
boolean Sequence is circular Boolean value Yes/No N
-squick1
-squick_sequence
boolean Read id and sequence only Boolean value Yes/No N
-sformat1
-sformat_sequence
string Input sequence format Any string  
-iquery1
-iquery_sequence
string Input query fields or ID list Any string  
-ioffset1
-ioffset_sequence
integer Input start position offset Any integer value 0
-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; B5BU39; Q8TBI5; Q8TDC1;
DT   01-APR-1993, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 3.
DT   16-MAY-2012, entry version 142.
DE   RecName: Full=Aquaporin-1;
DE            Short=AQP-1;
DE   AltName: Full=Aquaporin-CHIP;
DE   AltName: Full=Urine water channel;
DE   AltName: Full=Water channel protein for red blood cells and kidney proximal tubule;
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

See also

Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draw circular map of DNA constructs
echlorop Report presence of chloroplast transit peptides
elipop Predict lipoproteins
esignalp Report protein signal cleavage sites
etmhmm Reports transmembrane helices
iep Calculate the isoelectric point of proteins
lindna Draw linear maps of DNA constructs
pepinfo Plot amino acid properties of a protein sequence in parallel
pepnet Draw a helical net for a protein sequence
pepwheel Draw a helical wheel diagram for a protein sequence
plotorf Plot potential open reading frames in a nucleotide sequence
prettyplot Draw a sequence alignment with pretty formatting
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showfeat Display features of a sequence in pretty format
showpep Display protein sequences with features in pretty format
sigcleave Report on signal cleavage sites in a protein sequence
siggenlig Generate ligand-binding signatures from a CON file
sigscan Generate hits (DHF file) from a signature search
sixpack Display a DNA sequence with 6-frame translation and ORFs
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 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.

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

None