                                    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=d
a -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


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

   [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
   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
