
                             EMBOSS: showalign
     _________________________________________________________________
   
                               Program showalign
                                       
Function

   Displays a multiple sequence alignment
   
Description

   showalign displays an aligned set of protein or a nucleic acid
   sequences in a style suitable for publication.
   
   The output is sent to the screen by default for the user to view, but
   it can write the results to a file.
   
   The output highlights various differences or similarities between each
   of the sequences and a reference sequence by setting selected types of
   matches to a reference sequence to be '.' characters.
   
   The reference sequence can be either the calculated consensus sequence
   (the default) or it can be one of the set of aligned sequences,
   specified by either the ordinal number of that sequence in the input
   file, or by its name.
   
   The output sequences can be displayed in either the input order (the
   default) or they can be sorted in order of their similarity to the
   reference sequence or sorted alphabetically by their names.
   
   By using the '-show' option, the displayed sequences can either be
   shown as:
     * complete (-show=All),
     * only identical matches between the sequence and the reference
       sequence, all other positions being replaced by '.' characters
       (-show=Identities)
     * non-identical matches, with identical matches being replaced by
       '.' characters, similar matches are shown in lower case
       (-show=Non-identities)
     * similar matches, with non-similar matches being replaced by '.'
       characters, similar matches are shown in lower case
       (-show=Similarities)
     * dissimilar matches, with identical or similar matches being
       replaced by '.' characters (-show=Dissimilarities)
       
   A small table of the way these alignments are displayed illustrates
   this.
   If we have a reference protein sequence of "III" and a sequence
   aligned to this of "ILW", then we have an identical matching residue,
   then a similar one, then a dissimilar one.
   The different methods of display would give the following:
     _________________________________________________________________
   
Reference       III

All             ILw
Identical       I..
Non-id          .lW
Similar         Il.
Dissimilar      ..W
     _________________________________________________________________
   
   Changing the similar matches to lowercase can optionally be disable by
   using the option -nosimilarcase.
   
   The displayed sequence can be numbered by placing a ruler with ticks
   above the sequence.
   
   The width of a line can be set. The width of a margin to the left of
   the sequences that shows the sequence names can be set.
   
   Specified regions of the sequence can be displayed in uppercase to
   highlight them.
   
   The output can be formatted for HTML.
   
   If the output is being formatted for HTML, then specified regions of
   the sequence can be displayed in any valid HTML colours.
   
  The consensus line
  
   The consensus line can be displayed in a mixture of uppercase and
   lowercase symbols.
   
   The uppercase consensus symbol is meant to indicate that the consensus
   is strong and lowercase indicates that it is weak. In practice, I
   don't really like this feature and genarally turn it off.
   
   The cutoff for setting the case of the consensus is set by the
   qualifier '-setcase'. If the score of the matches is above this value,
   then the symbol is in uppercase, iot the score is below the -setcase
   value then the symbol is in lowercase.
   
   To put all of the consensus symbols into uppercase or lowercase, make
   -setcase very low (try -100000 ?) or very large (try 100000 ?).
   
Usage

   Here is a sample session with showalign:

% showalign
Display a multiple sequence alignment
Input sequence set: globin.seq
Output file [stdout]:
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpkv
HBB_MACFU ....P...n...T.....................................P....G....
HBD_HUMAN ....P...t..NA........A............................P....G....
HBB_RABIT ...sS.......A.......e.............................An...N....
HBB_BOVIN -M..A...a...AF....K..........-...................tA....N....
HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N....
HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG....
HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G....
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpkv

                  70        80        90       100       110       120
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus kahgkkvlxsfxdglXhldnlkgtfaklselhcdxxhvdpenfkllgnvlvivlaxhfgk
HBB_MACFU ........Ga.S...N..........q.......--...............C...H....
HBD_HUMAN ........Ga.S...A.........sq.......--.......r.......C...Rn...
HBB_RABIT ........Aa.Se..S..................KL.......r..........sH....
HBB_BOVIN ........D..Sn.mK...d......A.......KL...............v...Rn...
HBB_LAMGL ....S...N..G...S........y.........KL.......r.......v...R....
HBE_HUMAN ........T..G.AiKnm....PA..........--.............m..i..T....
HBE_RABIT ........T..G.AiKnm.....A..........--..............l....T....
Consensus kahgkkvlxsfxdglXhldnlkgtfaklselhcdxxhvdpenfkllgnvlvivlaxhfgk

                 130       140       150       160       170       180
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus eftpqvqaayqkvvagvanalahkyhxxxx
HBB_MACFU ..........................
HBD_HUMAN .....m....................
HBB_RABIT ..........................
HBB_BOVIN ....Vl..Df.............r..
HBB_LAMGL ....Dl.................r..ACDH
HBE_HUMAN ....e....w..l.sA
HBE_RABIT ....e....w..l.s...I.......
Consensus eftpqvqaayqkvvagvanalahkyhxxxx

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.
  [-outfile]           outfile    If you enter the name of a file here then
                                  this program will write the sequence details
                                  into that file.

   Optional qualifiers:
   -refseq             string     If you give the number in the alignment or
                                  the name of a sequence, it will be taken to
                                  be the reference sequence. The reference
                                  sequence is always show in full and is the
                                  one against which all the other sequences
                                  are compared. If this is set to 0 then the
                                  consensus sequence will be used as the
                                  reference sequence. By default the consensus
                                  sequence is used as the reference sequence.
   -[no]bottom         bool       If this is true then the refernce sequence
                                  is displayed at the bottom of the alignment
                                  as well as at the top.
   -show               menu       What to show
   -order              menu       Output order of the sequences
   -[no]similarcase    bool       If this is set True, then when -show is set
                                  to 'Similarities' or 'Non-identities' and a
                                  residue is similar but not identical to the
                                  reference sequence residue, it will be
                                  changed to lower-case. If -show is set to
                                  'All' then non-identical, non-similar
                                  residues will be changed to lower-case. If
                                  this is False then no change to the case of
                                  the residues is made on the basis of their
                                  similarity to the reference sequence.
   -matrix             matrix     Similarity scoring Matrix file
   -[no]consensus      bool       If this is true then the consensus line is
                                  displayed at the bottom.

   Advanced qualifiers:
   -uppercase          range      Regions to put in uppercase.
                                  If this is left blank, then the sequence
                                  case is left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99
   -[no]number         bool       If this option is true then a line giving
                                  the positions in the alignment is displayed
                                  every 10 characters above the alignment.
   -[no]ruler          bool       If this option is true then a ruler line
                                  marking every 5th and 10th character in the
                                  alignment is displayed.
   -width              integer    Width of sequence to display
   -margin             integer    This sets the length of the left-hand margin
                                  for sequence names. If the margin is set at
                                  0 then no margin and no names are
                                  displayed. If the margin is set to a value
                                  that is less than the length of a sequence
                                  name then the sequence name is displayed
                                  truncated to the length of the margin. If
                                  the margin is set to -1 then the minimum
                                  margin width that will allow all the
                                  sequence names to be displayed in full plus
                                  a space at the end of the name will
                                  automatically be selected.
   -[no]names          bool       Set this to be false if you do not wish to
                                  display the ID name of the sequences
   -html               bool       Use HTML formatting
   -highlight          range      Regions to colour if formatting for HTML.
                                  If this is left blank, then the sequence is
                                  left alone.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are followed by any valid HTML font
                                  colour.
                                  Examples of region specifications are:
                                  24-45 blue 56-78 orange
                                  1-100 green 120-156 red
                                  A file of ranges to colour (one range per
                                  line) can be specified as '@filename'.
   -plurality          float      Set a cut-off for the % of positive scoring
                                  matches below which there is no consensus.
                                  The default plurality is taken as 50% of the
                                  total weight of all the sequences in the
                                  alignment.
   -setcase            float      Sets the threshold for the scores of the
                                  positive matches above which the consensus
                                  is is upper-case and below which the
                                  consensus is in lower-case.
   -identity           float      Provides the facility of setting the
                                  required number of identities at a position
                                  for it to give a consensus. Therefore, if
                                  this is set to 100% only columns of
                                  identities contribute to the consensus.

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   

   Mandatory qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) The sequence alignment to be displayed. Readable
   sequences Required
   [-outfile]
   (Parameter 2) If you enter the name of a file here then this program
   will write the sequence details into that file. Output file stdout
   Optional qualifiers Allowed values Default
   -refseq If you give the number in the alignment or the name of a
   sequence, it will be taken to be the reference sequence. The reference
   sequence is always show in full and is the one against which all the
   other sequences are compared. If this is set to 0 then the consensus
   sequence will be used as the reference sequence. By default the
   consensus sequence is used as the reference sequence. Any string is
   accepted 0
   -[no]bottom If this is true then the refernce sequence is displayed at
   the bottom of the alignment as well as at the top. Yes/No Yes
   -show What to show
   A (All of the sequences)
   I (Identities between the sequences)
   N (Non-identities between the sequences)
   S (Similarities between the sequences)
   D (Dissimilarities between the sequences)
   N
   -order Output order of the sequences
   I (Input order - no change)
   A (Alphabetical order of the names)
   S (Similarity to the reference sequence)
   I
   -[no]similarcase If this is set True, then when -show is set to
   'Similarities' or 'Non-identities' and a residue is similar but not
   identical to the reference sequence residue, it will be changed to
   lower-case. If -show is set to 'All' then non-identical, non-similar
   residues will be changed to lower-case. If this is False then no
   change to the case of the residues is made on the basis of their
   similarity to the reference sequence. Yes/No Yes
   -matrix Similarity scoring Matrix file Comparison matrix file in
   EMBOSS data path EBLOSUM62 for protein
   EDNAFULL for DNA
   -[no]consensus If this is true then the consensus line is displayed at
   the bottom. Yes/No Yes
   Advanced qualifiers Allowed values Default
   -uppercase Regions to put in uppercase. If this is left blank, then
   the sequence case is left alone. A set of regions is specified by a
   set of pairs of positions. The positions are integers. They are
   separated by any non-digit, non-alpha character. Examples of region
   specifications are: 24-45, 56-78 1:45, 67=99;765..888
   1,5,8,10,23,45,57,99 Sequence range If this is left blank, then the
   sequence case is left alone.
   -[no]number If this option is true then a line giving the positions in
   the alignment is displayed every 10 characters above the alignment.
   Yes/No Yes
   -[no]ruler If this option is true then a ruler line marking every 5th
   and 10th character in the alignment is displayed. Yes/No Yes
   -width Width of sequence to display Integer 1 or more 60
   -margin This sets the length of the left-hand margin for sequence
   names. If the margin is set at 0 then no margin and no names are
   displayed. If the margin is set to a value that is less than the
   length of a sequence name then the sequence name is displayed
   truncated to the length of the margin. If the margin is set to -1 then
   the minimum margin width that will allow all the sequence names to be
   displayed in full plus a space at the end of the name will
   automatically be selected. Integer -1 or more -1
   -[no]names Set this to be false if you do not wish to display the ID
   name of the sequences Yes/No Yes
   -html Use HTML formatting Yes/No No
   -highlight Regions to colour if formatting for HTML. If this is left
   blank, then the sequence is left alone. A set of regions is specified
   by a set of pairs of positions. The positions are integers. They are
   followed by any valid HTML font colour. Examples of region
   specifications are: 24-45 blue 56-78 orange 1-100 green 120-156 red A
   file of ranges to colour (one range per line) can be specified as
   '@filename'. Sequence range full sequence
   -plurality Set a cut-off for the % of positive scoring matches below
   which there is no consensus. The default plurality is taken as 50% of
   the total weight of all the sequences in the alignment. Number from
   0.000 to 100.000 50.0
   -setcase Sets the threshold for the scores of the positive matches
   above which the consensus is is upper-case and below which the
   consensus is in lower-case. Any integer value 0
   -identity Provides the facility of setting the required number of
   identities at a position for it to give a consensus. Therefore, if
   this is set to 100% only columns of identities contribute to the
   consensus. Number from 0.000 to 100.000 0.0
   
Input file format

   showalign reads in a set of aligned protein or nucleic sequences.
   
   You can specifiy a file of ranges to display in uppercase by giving
   the '-uppercase' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-upper @myfile').
   
   The format of the range file is:
   
     * Comment lines start with '#' in the first column.
     * Comment lines and blank lines are ignored.
     * The line may start with white-space.
     * There are two positive (integer) numbers per line separated by one
       or more space or
     * TAB characters.
     * The second number must be greater or equal to the first number.
     * There can be optional text after the two numbers to annotate the
       line.
     * White-space before or after the text is removed.
       
   An example range file is:
   

# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

   You can specifiy a file of ranges to highlight in a different colour
   when outputting in HTML format (using the '-html' qualifier) by giving
   the '-highlight' qualifier the value '@' followed by the name of the
   file containing the ranges. (eg: '-highlight @myfile').
   
   The format of this file is very similar to the format of the above
   uppercase range file, except that the text after the start and end
   positions is used as the HTML colour name. This colour name is used
   'as is' when specifying the colour in HTML in a '' construct, (where
   'xxx' is the name of the colour).
   
   The standard names of HTML font colours are given in:
   http://http://www.w3.org/TR/REC-html40/types.html and
   http://www.ausmall.com.au/freegraf/ncolour2.htm and
   http://mindprod.com/htmlcolours.html (amongst other places).
   
   An example highlight range file is:
   

# this is my set of ranges
12   23         red
 4   5          darkturquoise
67   10348      #FFE4E1

Output file format

   showalign writes out a text file, optionally formatted for HTML.
   
   Some examples of different optional output styles follows:
     _________________________________________________________________
   
% showalign g.seq stdout -show=n
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU ....P...n...T.....................................P....G...
HBD_HUMAN ....P...t..NA........A............................P....G...
HBB_RABIT ...sS.......A.......e.............................An...N...
HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
% showalign g.seq stdout -show=a
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU VHLTpEEKNAVTtLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSpDAVMgNPK
HBD_HUMAN VHLTpEEKTAVnaLWGKVNVDaVGGEALGRLLVVYPWTQRFFESFGDLSSpDAVMgNPK
HBB_RABIT VHLSsEEKSAVTaLWGKVNVEEVGGEALGRLLVVYPWTQRFFESFGDLSSaNAVMnNPK
HBB_BOVIN -mLTaEEKAAVTafWGKVkVDEVGGEALG-LLVVYPWTQRFFESFGDLSTaDAVMnNPK
HBB_LAMGL VNLSgDEKNAVhgLWsKVkVDEVGGEALG-LLVVYPWTRRFFESFGDLSTaDAVMnNPK
HBE_HUMAN VHfTaEEKAAVTsLWsKMNVEEaGGEALGRLLVVYPWTQRFFDSFGNLSSpsAILgNPK
HBE_RABIT VHfTpEEKciISkqWGQVNIDEtGGEALGRLLVVYPWTQRFFDNFGNLSSssAIMgNPK
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
% showalign g.seq stdout -show=i
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU VHLT.EEK.AVT.LWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
HBD_HUMAN VHLT.EEK.AV..LWGKVNVD.VGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
HBB_RABIT VHL..EEKSAVT.LWGKVNV.EVGGEALGRLLVVYPWTQRFFESFGDLSS..AVM.NPK
HBB_BOVIN -.LT.EEK.AVT..WGKV.VDEVGGEALG-LLVVYPWTQRFFESFGDLS..DAVM.NPK
HBB_LAMGL V.L...EK.AV..LW.KV.VDEVGGEALG-LLVVYPWT.RFFESFGDLS..DAVM.NPK
HBE_HUMAN VH.T.EEK.AVT.LW.K.NV.E.GGEALGRLLVVYPWTQRFF.SFG.LSS..A...NPK
HBE_RABIT VH.T.EEK......WG.VN.DE.GGEALGRLLVVYPWTQRFF..FG.LSS..A.M.NPK
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
% showalign g.seq stdout -show=s
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU VHLT.EEKnAVT.LWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
HBD_HUMAN VHLT.EEKtAV..LWGKVNVD.VGGEALGRLLVVYPWTQRFFESFGDLSS.DAVM.NPK
HBB_RABIT VHLs.EEKSAVT.LWGKVNVeEVGGEALGRLLVVYPWTQRFFESFGDLSS.nAVM.NPK
HBB_BOVIN -.LT.EEKaAVT..WGKV.VDEVGGEALG-LLVVYPWTQRFFESFGDLSt.DAVM.NPK
HBB_LAMGL VnLs.dEKnAV..LW.KV.VDEVGGEALG-LLVVYPWTrRFFESFGDLSt.DAVM.NPK
HBE_HUMAN VH.T.EEKaAVT.LW.KmNVeE.GGEALGRLLVVYPWTQRFFdSFGnLSS..Ail.NPK
HBE_RABIT VH.T.EEK..is..WGqVNiDE.GGEALGRLLVVYPWTQRFFdnFGnLSS..AiM.NPK
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
% showalign g.seq stdout -show=d
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU ....P.......T.....................................P....G...
HBD_HUMAN ....P......NA........A............................P....G...
HBB_RABIT ....S.......A.....................................A....N...
HBB_BOVIN -M..A.......AF....K..........-....................A....N...
HBB_LAMGL ....G......HG..S..K..........-....................A....N...
HBE_HUMAN ..F.A.......S..S......A...........................PS...G...
HBE_RABIT ..F.P...CI..KQ........T...........................SS...G...
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
% showalign g.seq stdout -ref=1
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_MACFU VHLTPEEKNAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
HBD_HUMAN ........T..NA........A.....................................
HBB_RABIT ...sS...s...A.......e.............................An...N...
HBB_BOVIN -M..A...A...AF....K..........-...................tA....N...
HBB_LAMGL .n.sGd.....HG..S..K..........-........r..........tA....N...
HBE_HUMAN ..F.A...A...s..S.m..e.A...................d...n....S.il....
HBE_RABIT ..F.....CIisKQ..q..i..T...................dn..n...SS.i.....
HBB_MACFU VHLTPEEKNAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPK
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
Display a range of sequences in uppercase, everything else in lowercase
% showalign g.seq stdout -nocon -ref=1 -sl -upper 9-15 -nosimilarcaseDisplay a
multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
HBB_MACFU vhltpeekNAVTTLWgkvnvdevggealgrllvvypwtqrffesfgdlsspdavmgnpk
HBD_HUMAN ........T..NA........a.....................................
HBB_RABIT ...ss...S...A.......e.............................an...n...
HBB_BOVIN -m..a...A...AF....k..........-...................ta....n...
HBB_LAMGL .n.sgd.....HG..s..k..........-........r..........ta....n...
HBE_HUMAN ..f.a...A...S..s.m..e.a...................d...n....s.il....
HBE_RABIT ..f.....CIISKQ..q..i..t...................dn..n...ss.i.....
HBB_MACFU vhltpeekNAVTTLWgkvnvdevggealgrllvvypwtqrffesfgdlsspdavmgnpk
     _________________________________________________________________
     _________________________________________________________________
   
Alphabetical order
% showalign g.seq stdout -order=a
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
HBB_MACFU ....P...n...T.....................................P....G...
HBB_RABIT ...sS.......A.......e.............................An...N...
HBD_HUMAN ....P...t..NA........A............................P....G...
HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
In order of similarity to the reference sequence
% showalign g.seq stdout -order=s
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU ....P...n...T.....................................P....G...
HBB_RABIT ...sS.......A.......e.............................An...N...
HBD_HUMAN ....P...t..NA........A............................P....G...
HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
Format for HTML and highlight some inetersting regions in different colours
% showalign g.seq stdout -html -high '4-13 green 43-43 red 51-56 blue'
Display a multiple sequence alignment
                  10        20        30        40        50        60
          ----:----|----:----|----:----|----:----|----:----|----:----|
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
HBB_MACFU ....P...n...T.....................................P....G...
HBD_HUMAN ....P...t..NA........A............................P....G...
HBB_RABIT ...sS.......A.......e.............................An...N...
HBB_BOVIN -M..A...a...AF....K..........-...................tA....N...
HBB_LAMGL .n.sGd..n..HG..S..K..........-........r..........tA....N...
HBE_HUMAN ..F.A...a...S..S.m..e.A...................d...n...PS.ilG...
HBE_RABIT ..F.P...CIisKQ..q..i..T...................dn..n...SS.i.G...
Consensus vhltxeeksavtXlwgkvnvdevggealgrllvvypwtqrffesfgdlssxdavmxnpk
     _________________________________________________________________
     _________________________________________________________________
   
No consensus line at the bottom
No ruler line
No numbers line
Don't repeat the reference sequence at the bottom of the sequences
Use sequence 1 as the reference sequence
Display residues from position 10 to 30 only
% showalign g.seq stdout -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30
Display a multiple sequence alignment

HBB_MACFU AVTTLWGKVNVDEVGGEALGR
HBD_HUMAN ..NA........A........
HBB_RABIT ...A.......e.........
HBB_BOVIN ...AF....K..........-
HBB_LAMGL ..HG..S..K..........-
HBE_HUMAN ...s..S.m..e.A.......
HBE_RABIT IisKQ..q..i..T.......
     _________________________________________________________________
   
Data files

   showalign reads in scoring matrices to determine the consesnus
   sequence and to determine which matches are similar or not.
   
   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

   None.
   
References

   None.
   
Warnings

   None.
   
Diagnostic Error Messages

   None.
   
Exit status

   It always exits with status 0.
   
Known bugs

   None.
   
See also

   Program name Description
   abiview Reads ABI file and display the trace
   cirdna Draws circular maps of DNA constructs
   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 Plots the quality of conservation of a sequence alignment
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showdb Displays information on the currently available databases
   showfeat Show features of a sequence
   showseq Display a sequence with features, translation etc
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   tranalign Align nucleic coding regions given the aligned proteins
   
Author(s)

   This application was written by Gary Williams
   (gwilliam@hgmp.mrc.ac.uk)
   
History

   Written (23 May 2001) - Gary Williams
   
Target users

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