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prettyplot |
% prettyplot -resbreak=10 -boxcol -consensus -plurality=3 Displays aligned sequences, with colouring and boxing Input (aligned) sequence set: globins.msf Graph type [x11]: cps Created prettyplot.ps |
Go to the input files for this example
Go to the output files for this example
Example 2
% prettyplot globins.msf -plurality=3 -docolour Displays aligned sequences, with colouring and boxing Graph type [x11]: cps Created prettyplot.ps |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequences] seqset (Aligned) sequence set filename and optional
format, or reference (input USA)
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
Additional (Optional) qualifiers:
-matrixfile matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-residuesperline integer [50] The number of residues to be displayed
on each line (Any integer value)
-resbreak integer [Same as -residuesperline to give no breaks]
Residues before a space (Integer 1 or more)
-[no]ccolours boolean [Y] Colour residues by their consensus
value.
-cidentity string [RED] Colour to display identical residues
(RED) (Any string is accepted)
-csimilarity string [GREEN] Colour to display similar residues
(GREEN) (Any string is accepted)
-cother string [BLACK] Colour to display other residues
(BLACK) (Any string is accepted)
-docolour boolean [N] Colour residues by table oily, amide
etc.
-shade string Set to BPLW for normal shading
(black, pale, light, white)
so for pair = 1.5,1.0,0.5 and shade = BPLW
Residues score Colour
1.5 or over... BLACK (B)
1.0 to 1.5 ... BROWN (P)
0.5 to 1.0 ... WHEAT (L)
under 0.5 .... WHITE (W)
The only four letters allowed are BPLW, in
any order. (Any string up to 4 characters,
matching regular expression
/^([BPLW]{4})?$/)
-pair array [1.5,1.0,0.5] Values to represent identical
similar related
-identity integer [0] Only match those which are identical in
all sequences. (Integer 0 or more)
-[no]box boolean [Y] Display prettyboxes
-boxcol boolean [N] Colour the background in the boxes
-boxcolval string [GREY] Colour to be used for background.
(GREY) (Any string is accepted)
-[no]name boolean [Y] Display the sequence names
-maxnamelen integer [10] Margin size for the sequence name. (Any
integer value)
-[no]number boolean [Y] Display the residue number
-[no]listoptions boolean [Y] Display the date and options used
-plurality float [Half the total sequence weighting]
Plurality check value (totweight/2) (Any
numeric value)
-consensus boolean [N] Display the consensus
-[no]collision boolean [Y] Allow collisions in calculating
consensus
-alternative menu [0] Values are 0:Normal collision check.
(default)
1:Compares identical scores with the max
score found. So if any other residue matches
the identical score then a collision has
occurred.
2:If another residue has a greater than or
equal to matching score and these do not
match then a collision has occurred.
3:Checks all those not in the current
consensus.If any of these give a top score
for matching or identical scores then a
collision has occured. (Values: 0 (Normal
collision check. (default)); 1 (Compares
identical scores with the max score found.
So if any other residue matches the
identical score then a collision has
occurred.); 2 (If another residue has a
greater than or equal to matching score and
these do not match then a collision has
occurred.); 3 (Checks all those not in the
current consensus.If any of these give a top
score for matching or identical scores then
a collision has occured.))
-showscore integer [-1] Print residue scores (Any integer
value)
-portrait boolean [N] Set page to Portrait
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequences" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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 standard output
-filter boolean Read standard input, write 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. 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
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| [-sequences] (Parameter 1) |
(Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required | ||||||||
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 | ||||||||
| Additional (Optional) qualifiers | Allowed values | Default | |||||||||
| -matrixfile | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
||||||||
| -residuesperline | The number of residues to be displayed on each line | Any integer value | 50 | ||||||||
| -resbreak | Residues before a space | Integer 1 or more | Same as -residuesperline to give no breaks | ||||||||
| -[no]ccolours | Colour residues by their consensus value. | Boolean value Yes/No | Yes | ||||||||
| -cidentity | Colour to display identical residues (RED) | Any string is accepted | RED | ||||||||
| -csimilarity | Colour to display similar residues (GREEN) | Any string is accepted | GREEN | ||||||||
| -cother | Colour to display other residues (BLACK) | Any string is accepted | BLACK | ||||||||
| -docolour | Colour residues by table oily, amide etc. | Boolean value Yes/No | No | ||||||||
| -shade | Set to BPLW for normal shading (black, pale, light, white) so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over... BLACK (B) 1.0 to 1.5 ... BROWN (P) 0.5 to 1.0 ... WHEAT (L) under 0.5 .... WHITE (W) The only four letters allowed are BPLW, in any order. | Any string up to 4 characters, matching regular expression /^([BPLW]{4})?$/ | An empty string is accepted | ||||||||
| -pair | Values to represent identical similar related | List of floating point numbers | 1.5,1.0,0.5 | ||||||||
| -identity | Only match those which are identical in all sequences. | Integer 0 or more | 0 | ||||||||
| -[no]box | Display prettyboxes | Boolean value Yes/No | Yes | ||||||||
| -boxcol | Colour the background in the boxes | Boolean value Yes/No | No | ||||||||
| -boxcolval | Colour to be used for background. (GREY) | Any string is accepted | GREY | ||||||||
| -[no]name | Display the sequence names | Boolean value Yes/No | Yes | ||||||||
| -maxnamelen | Margin size for the sequence name. | Any integer value | 10 | ||||||||
| -[no]number | Display the residue number | Boolean value Yes/No | Yes | ||||||||
| -[no]listoptions | Display the date and options used | Boolean value Yes/No | Yes | ||||||||
| -plurality | Plurality check value (totweight/2) | Any numeric value | Half the total sequence weighting | ||||||||
| -consensus | Display the consensus | Boolean value Yes/No | No | ||||||||
| -[no]collision | Allow collisions in calculating consensus | Boolean value Yes/No | Yes | ||||||||
| -alternative | Values are 0:Normal collision check. (default) 1:Compares identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3:Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. |
|
0 | ||||||||
| -showscore | Print residue scores | Any integer value | -1 | ||||||||
| -portrait | Set page to Portrait | Boolean value Yes/No | No | ||||||||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||||
| (none) | |||||||||||
!!AA_MULTIPLE_ALIGNMENT 1.0
../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 ..
Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.61
Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.65
Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.65
Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.83
Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 1.00
Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.91
Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.43
//
1 50
HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD
51 100
HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN
101 150
HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA
151 164
HBB_HUMAN NALAHKYH~~~~~~
HBB_HORSE NALAHKYH~~~~~~
HBA_HUMAN TVLTSKYR~~~~~~
HBA_HORSE TVLTSKYR~~~~~~
MYG_PHYCA KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~
|
![[prettyplot results]](prettyplot.2.prettyplot.gif)
For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
| Program name | Description |
|---|---|
| abiview | Reads ABI file and display the trace |
| cirdna | Draws circular maps of DNA constructs |
| edialign | Local multiple alignment of sequences |
| emma | Multiple alignment program - interface to ClustalW program |
| infoalign | Information on a multiple sequence alignment |
| lindna | Draws linear maps of DNA constructs |
| pepnet | Displays proteins as a helical net |
| pepwheel | Shows protein sequences as helices |
| plotcon | Plot quality of conservation of a sequence alignment |
| prettyseq | Output sequence with translated ranges |
| remap | Display sequence with restriction sites, translation etc |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| showfeat | Show features of a sequence |
| showseq | Display a sequence with features, translation etc |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| textsearch | Search sequence documentation. Slow, use SRS and Entrez! |
| tranalign | Align nucleic coding regions given the aligned proteins |
Many features were first implemented in the EGCG program "prettyplot" by
Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
The original suggestions for the PrettyPlot program were from Denis Duboule and Sigfried Labeit at EMBL. Gert Vriend added the star marking. Rita Grandori suggested the -NOCOLLISION option.
![[prettyplot results]](prettyplot.1.prettyplot.gif)