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prettyplot
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Draw a sequence alignment with pretty formatting
Description
prettyplot draws a plot of the input sequence alignment. The sequences
are rendered in pretty formatting on the specified graphics device.
Drawing options control the appearance of the image, such as boxes,
colour and shading for highlighting conserved regions.
Usage
Here is a sample session with prettyplot
% prettyplot -blocksperline=5 -boxcol -consensus -ratio=0.59
Draw a sequence alignment with pretty formatting
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 -ratio=0.59 -docolour
Draw a sequence alignment with pretty formatting
Graph type [x11]: cps
Created prettyplot.ps
Go to the output files for this example
Command line arguments
Draw a sequence alignment with pretty formatting
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequences] seqset (Aligned) sequence set filename and optional
format, or reference (input USA)
-graph graph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tek, tekt, none, data, xterm, png, gif, pdf,
svg)
Additional (Optional) qualifiers:
-matrixfile matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-residuesperline integer [50] The number of residues to be displayed
on each line (Any integer value)
-blocksperline integer [1] Blocks of residues on each line (Integer
1 or more)
-[no]ccolours boolean [Y] Colour residues by their consensus
value.
-cidentity string [RED] Colour to display identical residues
(RED) (Any string)
-csimilarity string [GREEN] Colour to display similar residues
(GREEN) (Any string)
-cother string [BLACK] Colour to display other residues
(BLACK) (Any string)
-docolour boolean [N] Colour residues by table oily, amide
etc.
-shade string Set to BPLW for normal shading
(black, pale, light, white)
so for pair = 1.5,1.0,0.5 and shade = BPLW
Residues score Colour
1.5 or over... BLACK (B)
1.0 to 1.5 ... BROWN (P)
0.5 to 1.0 ... WHEAT (L)
under 0.5 .... WHITE (W)
The only four letters allowed are BPLW, in
any order. (Any string up to 4 characters,
matching regular expression
/^([BPLW]{4})?$/)
-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]doboxes boolean [Y] Display prettyboxes
-boxcol boolean [N] Colour the background in the boxes
-boxuse string [GREY] Colour to be used for background.
(GREY) (Any string)
-[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
-ratio float [0.5] Plurality ratio for a consensus match
(Number from 0.000 to 1.000)
-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
-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
prettyplot reads aligned protein sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, where 'xxx' is replaced by the name of the required
format. The available format names are: gff (gff3), gff2, embl (em),
genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
Input files for usage example
File: globins.msf
!!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~~~
Output file format
The output is to the specified graphics device.
The results can be output in one of several formats by using the
command-line qualifier -graph xxx, where 'xxx' is replaced by the name
of the required device. Support depends on the availability of
third-party software packages.
The device names that output to a file are: ps (postscript), cps
(colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.
The other available device names are: meta, x11 (xwindows), tek
(tek4107t), tekt (tektronix), xterm, text.
Output can be turned off by specifying none (null).
See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
information on supported devices.
Output files for usage example
Graphics File: prettyplot.ps
[prettyplot results]
Output files for usage example 2
Graphics File: prettyplot.ps
[prettyplot results]
Data files
Prettyplot uses a comparison matrix file to calculate similarity to the
consensus.
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:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
A consesnsus sequence is calculated for the alignment and individual
sequences compared to the consensus using the specified comparison
matrix file. The default matrix for protein sequences is EBLOSUM62 and
for nucleotide sequences is EDNAFULL. The drawing options render
conserved sites and regions identified from the comparisons. For
example, residues in a sequence are classed as "identical", "similar"
or "other" to the consensus depending on user-specified thresholds of
sequence similarity (-pair option). Residues in each class are rendered
red, green and black by default (this can be changed).
There are other more general drawing options, for example, controlling
the number of residues displayed per line, background shading and
whether to display sequence names or not.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It exits with status 0 unless an error is reported.
Known bugs
Portrait mode does not cover the whole page! This is a "feature" in
plplot.
See also
Program name Description
abiview Display the trace in an ABI sequencer file
cirdna Draw circular map of DNA constructs
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
iep Calculate the isoelectric point of proteins
infoalign Display basic information about a multiple sequence alignment
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
plotcon Plot conservation of a sequence alignment
plotorf Plot potential open reading frames in a nucleotide sequence
prettyseq Write a nucleotide sequence and its translation to file
remap Display restriction enzyme binding sites in a nucleotide sequence
showalign Display a multiple sequence alignment in pretty format
showfeat Display features of a sequence in pretty format
showpep Display protein sequences with features in pretty format
sixpack Display a DNA sequence with 6-frame translation and ORFs
tranalign Generate an alignment of nucleic coding regions from aligned
proteins
Author(s)
Ian Longden formerly at:
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
CB10 1SA, UK.
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
Many features were first implemented in the EGCG program "prettyplot"
by Peter Rice
European Bioinformatics Institute, Wellcome Trust Genome Campus,
Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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.
History
Completed 5th May 1999.
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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