                                    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
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


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 (c) 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
