EMBOSS: plotcon manual

plotcon

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

Plot conservation of a sequence alignment

Description

plotcon reads a sequence alignment and draws a plot of the sequence conservation within windows over the alignment.

Algorithm

Sequence conservation is calculated for windows of a specified length over the alignment. Within a window, the similarity of any one position is taken to be the average of all the possible pairwise substitution scores of the bases or residues at that position. The pairwise substitution scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted.

The average similarity is calculated by:


Av. Sim. =       sum( Mij*wi + Mji*wj  )
                      -------------------
                  (Nseq*Wsize)*((Nseq-1)*Wsize)

sum - over column*window size
w - sequence weighting
M - matrix comparison table
i,j - with respect to residue i or j
Nseq - number of sequences in the alignment
Wsize - window size

Usage

Here is a sample session with plotcon


% plotcon -sformat msf globins.msf -graph cps 
Plot conservation of a sequence alignment
Window size [4]: 

Created plotcon.ps

Go to the input files for this example
Go to the output files for this example

Command line arguments

Plot conservation of a sequence alignment
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing a sequence alignment
   -winsize            integer    [4] Number of columns to average alignment
                                  quality over. The larger this value is, the
                                  smoother the plot will be. (Any integer
                                  value)
   -graph              xygraph    [$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:
   -scorefile          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.

   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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-sequences] (Parameter 1)	seqset	File containing a sequence alignment	Readable set of sequences	Required
-winsize	integer	Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be.	Any integer value	4
-graph	xygraph	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
-scorefile	matrix	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
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin1 -sbegin_sequences	integer	Start of each sequence to be used	Any integer value	0
-send1 -send_sequences	integer	End of each sequence to be used	Any integer value	0
-sreverse1 -sreverse_sequences	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_sequences	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_sequences	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_sequences	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_sequences	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_sequences	boolean	Make upper case	Boolean value Yes/No	N
-scircular1 -scircular_sequences	boolean	Sequence is circular	Boolean value Yes/No	N
-squick1 -squick_sequences	boolean	Read id and sequence only	Boolean value Yes/No	N
-sformat1 -sformat_sequences	string	Input sequence format	Any string
-iquery1 -iquery_sequences	string	Input query fields or ID list	Any string
-ioffset1 -ioffset_sequences	integer	Input start position offset	Any integer value	0
-sdbname1 -sdbname_sequences	string	Database name	Any string
-sid1 -sid_sequences	string	Entryname	Any string
-ufo1 -ufo_sequences	string	UFO features	Any string
-fformat1 -fformat_sequences	string	Features format	Any string
-fopenfile1 -fopenfile_sequences	string	Features file name	Any string
"-graph" associated xygraph qualifiers
-gprompt	boolean	Graph prompting	Boolean value Yes/No	N
-gdesc	string	Graph description	Any string
-gtitle	string	Graph title	Any string
-gsubtitle	string	Graph subtitle	Any string
-gxtitle	string	Graph x axis title	Any string	Relative Residue Position
-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

plotcon reads a set of gapped, aligned sequences.

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

A graph of the quality of the alignment is dispalyed on the specifed graphics device.

Output files for usage example

Graphics File: plotcon.ps

[plotcon results]

Data files

It reads in the specified similarity matrix.

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

The program is useful for visualising the quality of alignment along its length. This can give a qualitative insight into where there are regions of conservation in a group of aligned sequences.

Note that you should only compare the results of two runs of plotcon if you use the same window size in each. This is because the 'similarity score' units that are output are very sensitive to the size of the window. A large window (e.g. 100) gives a nice, smooth curve, and very low 'similarity score' units, whereas a small window (e.g. 4) gives a very spikey, noisy plot with 'similarity score' units of a round 1.00

References

None.

Warnings

plotcon does not distinguish between aligned and unaligned sets of sequences. If the input set of sequences is unaligned, the output will in most cases lack much biological meaning.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
edialign	Local multiple alignment of sequences
emma	Multiple sequence alignment (ClustalW wrapper)
infoalign	Display basic information about a multiple sequence alignment
prettyplot	Draw a sequence alignment with pretty formatting
showalign	Display a multiple sequence alignment in pretty format
tranalign	Generate an alignment of nucleic coding regions from aligned proteins

Author(s)

Tim Carver formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

Written (Sept 2000) - Tim Carver.

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: globins.msf

Output file format

Output files for usage example

Graphics File: plotcon.ps

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments