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showalign
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
Display a multiple sequence alignment in pretty format
Description
showalign reads a set of aligned protein or a nucleic acid sequences,
and writes them to file (or screen) in a style suitable for
publication. Similarities and differences of each sequence to a
reference sequence are highlighted for specified types of matches. The
reference sequence can be the calculated consensus sequence (default)
or one of the input set (specified by name or the ordinal number of
that sequence in the file). The output sequences can be displayed in
either the input order (the default), sorted in order of their
similarity to the reference sequence, or sorted alphabetically by their
names. There are many other options to control the content and format
of the output.
Usage
Here is a sample session with showalign
% showalign
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the input files for this example
Go to the output files for this example
Example 2
Display the sequences in order of similarity to the reference sequence
% showalign -order=s
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 3
Format for HTML and highlight some interesting regions in different
colours:
% showalign -html -high "4-13 green 43-43 red 51-56 blue"
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 4
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 -nocon -norule -nonum -nobot -ref=1 -sb=10 -send=30
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 5
Show non-identities between the sequences
% showalign -show=n
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Example 6
Show all of the sequences
% showalign -show=a
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 7
Show identities between the sequences
% showalign -show=i
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 8
Show similarities between the sequences
% showalign -show=s
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 9
Show dissimilarities between the sequences
% showalign -show=d
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 10
Use the first sequence as the reference to compare to:
% showalign -ref=1
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 11
Show a range of sequences in uppercase, everything else in lowercase
% showalign -nocon -ref=1 -sl -upper 9-15 -nosimilarcase
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Example 12
Display the sequences in alphabetic order:
% showalign -order=a
Display a multiple sequence alignment in pretty format
Input (aligned) sequence set: globins.msf
Output file [globins.showalign]:
Go to the output files for this example
Command line arguments
Display a multiple sequence alignment in pretty format
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqset The sequence alignment to be displayed.
[-outfile] outfile [*.showalign] Output file name
Additional (Optional) qualifiers:
-matrix 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.
-refseq string [0] 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 shown 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)
-[no]bottom boolean [Y] If this is true then the reference
sequence is displayed at the bottom of the
alignment instead of the top.
-show menu [N] What to show (Values: 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))
-order menu [I] Output order of the sequences (Values: I
(Input order - no change); A (Alphabetical
order of the names); S (Similarity to the
reference sequence))
-[no]similarcase boolean [Y] 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.
-[no]consensus boolean [Y] If this is true then the consensus line
is displayed.
Advanced (Unprompted) qualifiers:
-uppercase range [If this is left blank, then the sequence
case is left alone.] 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 boolean [Y] If this option is true then a line
giving the positions in the alignment is
displayed every 10 characters above the
alignment.
-[no]ruler boolean [Y] If this option is true then a ruler line
marking every 5th and 10th character in the
alignment is displayed.
-width integer [60] Width of sequence to display (Integer 1
or more)
-margin integer [-1] 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)
-html boolean [N] Use HTML formatting
-highlight range [(full sequence)] 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 [50.0] 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)
-setcase float [@( $(sequence.totweight) / 2)] Sets the
threshold for the scores of the positive
matches above which the consensus is in
upper-case and below which the consensus is
in lower-case. By default this is set to be
half of the (weight-adjusted) number of
sequences in the alignment. (Any numeric
value)
-identity float [0.0] 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)
-[no]gaps boolean [Y] If this option is true then gap
characters can appear in the consensus. The
alternative is 'N' for nucleotide, or 'X'
for protein
Associated qualifiers:
"-sequence" 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
"-outfile" associated qualifiers
-odirectory2 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
showalign reads in a set of aligned protein or nucleic 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~~~
You can specify 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 specify 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#h-6.5
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.
Output files for usage example
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
HBB_HORSE --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
HBA_HORSE --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
MYG_PHYCA -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HUMAN F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
MYG_PHYCA EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HUMAN C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBA_HORSE C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
MYG_PHYCA AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 2
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
HBB_HORSE --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBA_HORSE --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
HBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
MYG_PHYCA -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
HBA_HUMAN F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
MYG_PHYCA EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HORSE C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
HBA_HUMAN C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
MYG_PHYCA AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 3
File: globins.showalign
<pre>
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN ---<font color=green>-----VH.tP</font>E.K.A.TaL.G.V.-VD....E..GR-.L<f
ont color=red>V</font>vY.WT.R<font color=blue>..Es.G</font>D..T
HBB_HORSE ---<font color=green>-----VQ..G</font>E.KaA.LaL.D.V.-EE....E..GR-.L<f
ont color=red>V</font>vY.WT.R<font color=blue>..Ds.G</font>D..N
HBA_HUMAN ---<font color=green>----------</font>-VL.PADKTNV.AA-WGk..AH.GEYGAE<f
ont color=red>A</font>lERMFLS<font color=blue>.PT.KT</font>YFPH
HBA_HORSE ---<font color=green>----------</font>-VL.AADKTNV.AA-WSk...H.GEYGAE<f
ont color=red>A</font>lERMFLG<font color=blue>.PT.KT</font>YFPH
MYG_PHYCA ---<font color=green>----VLSEGE</font>WqLVLHVWAKVeAd-VAGH.QDI.IR-.F<f
ont color=red>K</font>SH.ETLE<font color=blue>K.DR.K</font>H.KT
GLB5_PETMA PIV<font color=green>DTGSVAP..A</font>A.KtKiR.A.APVYSTY.TS.VDiLVKFF<f
ont color=red>T</font>ST.AA.E<font color=blue>..PK.K</font>G.tT
LGB2_LUPLU ---<font color=green>-----GA.tE</font>SqAaL.K.S.EeF.ANIPKHTHRFFILvL<f
ont color=red>E</font>.A.AAkD<font color=blue>L.SFLK</font>GT.E
Consensus xxx<font color=green>xxxxxxxLSx</font>xExSxVxSxWxKxNxxxEVGGxALxxxLx<f
ont color=red>x</font>IxPxxQx<font color=blue>FFxTFx</font>xLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
HBB_HORSE PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBA_HUMAN F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
MYG_PHYCA EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
HBB_HORSE V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBA_HUMAN C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBA_HORSE C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
MYG_PHYCA AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
</pre>
Output files for usage example 4
File: globins.showalign
HBB_HUMAN HLTPEEKSAVTALWGKVN-VD
HBB_HORSE Q.sG...a..L...D...-Ee
HBA_HUMAN -----VL.PADKTNV.AA-WG
HBA_HORSE -----VL..ADKTNV.AA-WS
MYG_PHYCA SEGEWqLVLHVWAKVeAd-.A
GLB5_PETMA P.sAA..tKiRsA.AP.YSTY
LGB2_LUPLU A..ESqAaL.KsS.EeF.ANI
Output files for usage example 6
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------vhLTpeEkSaVtAlWgKvN-vdEVGGeALgr-LlvVyPwtQrFFeSFgdLSt
HBB_HORSE --------vqLSgeEkAaVlAlWdKvN-eeEVGGeALgr-LlvVyPwtQrFFdSFgdLSn
HBA_HUMAN --------------vlSpadktnvKaa-wgKVGahAgeygaeaLermflsFptTktyfph
HBA_HORSE --------------vlSaadktnvKaa-wsKVGGhAgeygaeaLermflgFptTktyfph
MYG_PHYCA -------vlsegewQlvlhvwakvEaD-vaghGqdiLir-LfkshPetlekFdrFkhLkt
GLB5_PETMA pivdtgsvapLSaaEkTkIrSaWapvystyEtsGvdIlvkfftstPaaQeFFpkFkgLTt
LGB2_LUPLU --------gaLTesQaAlVkSsWeEfNanipkhthrffilVleIaPaaKdlFsflkgtSe
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN pDaVmGNpKVKaHGKKVLgAfsDgLaHLDNLKgtfAtLSELHcdKLh--VDPeNFRLLgN
HBB_HORSE pgaVmGNpKVKaHGKKVLhSfgEgVhHLDNLKgtfAaLSELHcdKLh--VDPeNFRLLgN
HBA_HUMAN fDlshGSaQVKgHGKKVadALtNaVaHVDDMpnalSaLSDLHAhKLR--VDPvNFKLLsH
HBA_HORSE fDlshGSaQVKaHGKKVgdALtlaVgHLDDLpgalSnLSDLHAhKLR--VDPvNFKLLsH
MYG_PHYCA eaeMkaSedLKkHGvtVLtALgaiLkkkghhEaelkpLAqsHAtKhK--IpikylEfIse
GLB5_PETMA aDqLkkSadVRwHaERIInAVnDaVasMDDtEkmsmkLrDLsgkhaK--sfqvDpQyfkv
LGB2_LUPLU vpqnnpelQahagkvfkLvyeaaiqlqVtgVvvtdAtLkNLgSvhVskgVadaHFpVVke
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN vLVcVLAhHfgkEFTPpVqAAyqKvVAgVAnaLahKYh------
HBB_HORSE vLVvVLArHfgkDFTPELqASyqKvVAgVAnaLahKYh------
HBA_HUMAN cLLvtLAaHlpaEFTPaVhASLdKfLAsVStvLtsKYr------
HBA_HORSE cLLstLAvHlpnDFTPaVhASLdKfLSsVStvLtsKYr------
MYG_PHYCA aIIhVLhsrhpgDFgaDaqgAMnKaLelfrkdIaaKYkelgyqg
GLB5_PETMA laavIadtvaagDagfEklmSMiciLlrsAy-------------
LGB2_LUPLU aILktIkevvgakWSeELnSAwtiaydeLAivIkkEmndaa---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 7
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------..L...E.S.V...W.K.N-..EVGG.AL..-L....P..Q.FF..F..LS.
HBB_HORSE --------..LS..E...V...W.K.N-..EVGG.AL..-L....P..Q.FF..F..LS.
HBA_HUMAN --------------..S.......K..-...VG..A..............F..T......
HBA_HORSE --------------..S.......K..-...VGG.A..............F..T......
MYG_PHYCA -------....................-....G...L..-L....P.....F..F..L..
GLB5_PETMA ..........LS..E.....S.W.......E..G...........P..Q.FF..F..L..
LGB2_LUPLU --------..L.......V.S.W...N................I.P.....F......S.
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN .D...G...VK.HGKKVL.A..D...HLD.L....A.LS.LH..KL.--VDP.NF.LL..
HBB_HORSE .....G...VK.HGKKVL......V.HLD.L....A.LS.LH..KL.--VDP.NF.LL..
HBA_HUMAN .D...GS.QVK.HGKKV..AL...V.H.DD.......LSDLHA.KLR--VDP.NFKLL.H
HBA_HORSE .D...GS.QVK.HGKKV..AL...V.HLDDL......LSDLHA.KLR--VDP.NFKLL.H
MYG_PHYCA ...M..S...K.HG..VL.AL..........E.....L...HA.K..--...........
GLB5_PETMA .D....S..V..H......A..D.V...DD.E.....L.DL......--...........
LGB2_LUPLU ........Q........L.................A.L..L........V....F.....
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN .L..VLA.H....FTP.V.A...K..A.VA..L..KY.------
HBB_HORSE .L..VLA.H...DFTPE..AS..K..A.VA..L..KY.------
HBA_HUMAN .LL..LA.H....FTP.V.AS..K.LA.V...L..KY.------
HBA_HORSE .LL..LA.H...DFTP.V.AS..K.L..V...L..KY.------
MYG_PHYCA ....VL......DF.......M.K.L.........KY.......
GLB5_PETMA ............D...E...SM...L...A.-------------
LGB2_LUPLU ..L.............E............A...........---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 8
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------..Lt..E.S.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.
HBB_HORSE --------..LS..E.a.V.a.W.K.N-..EVGG.AL..-L..v.P..Q.FF.sF..LS.
HBA_HUMAN --------------..S.......K..-..kVG..A.......l......F..T......
HBA_HORSE --------------..S.......K..-..kVGG.A.......l......F..T......
MYG_PHYCA -------.......q.........e.d-....G...L..-L....P.....F..F..L..
GLB5_PETMA ..........LS..E.t.i.S.W.......E..G..i........P..Q.FF..F..Lt.
LGB2_LUPLU --------..Lt..q.a.V.S.W.e.N.............v..I.P..k..F......S.
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN .D.v.Gn.kVK.HGKKVL.A..D.l.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.n
HBB_HORSE ...v.Gn.kVK.HGKKVL.s..e.V.HLDnLk...A.LSeLH..KL.--VDP.NFrLL.n
HBA_HUMAN .D...GS.QVK.HGKKV..AL.n.V.HvDDm....s.LSDLHA.KLR--VDP.NFKLL.H
HBA_HORSE .D...GS.QVK.HGKKV..AL...V.HLDDL....s.LSDLHA.KLR--VDP.NFKLL.H
MYG_PHYCA ...M..S..lK.HG..VL.AL...l......E.....La..HA.K.k--i.....e.i..
GLB5_PETMA .D.l..S..Vr.H.erii.Av.D.V..mDD.E.....L.DL.....k--....d.q....
LGB2_LUPLU ........Q........L.........v..v....A.L.nL.s..v...V...hF.vv..
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN .Lv.VLA.H...eFTP.V.Aa..K.vA.VA..L..KY.------
HBB_HORSE .Lv.VLA.H...DFTPEl.AS..K.vA.VA..L..KY.------
HBA_HUMAN .LL..LA.H...eFTP.V.ASl.K.LA.Vs..L..KY.------
HBA_HORSE .LL..LA.H...DFTP.V.ASl.K.Ls.Vs..L..KY.------
MYG_PHYCA .ii.VL......DF..d...aM.K.L......i..KY.......
GLB5_PETMA ....i.......D...E...SM...L...A.-------------
LGB2_LUPLU .iL..i.......ws.El.sa.......lA..i..e.....---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 9
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN --------VH..PE.K.A.T.L.G.V.-VD....E..GR-.LV.Y.WT.R..E..GD..T
HBB_HORSE --------VQ..GE.K.A.L.L.D.V.-EE....E..GR-.LV.Y.WT.R..D..GD..N
HBA_HUMAN --------------VL.PADKTNV.AA-WG...AH.GEYGAEA.ERMFLS.PT.KTYFPH
HBA_HORSE --------------VL.AADKTNV.AA-WS....H.GEYGAEA.ERMFLG.PT.KTYFPH
MYG_PHYCA -------VLSEGEW.LVLHVWAKV.A.-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
GLB5_PETMA PIVDTGSVAP..AA.K.K.R.A.APVYSTY.TS.VD.LVKFFTST.AA.E..PK.KG..T
LGB2_LUPLU --------GA..ES.A.L.K.S.E.F.ANIPKHTHRFFIL.LE.A.AA.DL.SFLKGT.E
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
HBB_HUMAN P.A.M..P...A......G.FS.G.A......GTF.T.....CD..H--...E.....G.
HBB_HORSE PGA.M..P...A......H.FG.G.H......GTF.A.....CD..H--...E.....G.
HBA_HUMAN F.LSH..A...G.....AD..T.A.A.....PNAL.A......H...--...V.....S.
HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGAL.N......H...--...V.....S.
MYG_PHYCA EAE.KA.ED..K..VT..T..GAI.KKKGHH.AELKP..QS..T.H.--.PIKYL.F.SE
GLB5_PETMA A.Q.KK.AD..W.A....N..N.A.AS...T.KMSMK.R..SGKHA.--SFQV.P.YFKV
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQ.TG.VVTD.T.K..G.VH.SKG.ADA..P..KE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
HBB_HUMAN V..C...H.FGK....P.Q..YQ.V..G..NA.AH..H------
HBB_HORSE V..V...R.FGK......Q..YQ.V..G..NA.AH..H------
HBA_HUMAN C..VT..A.LPA....A.H...D.F..S..TV.TS..R------
HBA_HORSE C..ST..V.LPN....A.H...D.F..S..TV.TS..R------
MYG_PHYCA A..H..HSRHPG..GA.AQG..N.A.ELFRKD.AA..KELGYQG
GLB5_PETMA LAAV.ADTVAAG.AGF.KLM..ICI.LRS.Y-------------
LGB2_LUPLU A..KT.KEVVGAK..E..N..WTIAYDE..IV.KK.MNDAA---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 10
File: globins.showalign
10 20 30 40 50
...v....----:----|----:----.|----:----|.----:----|----:----|
HBB_HUMAN --------VHLTPEEKSAVTALWGKVN-VDEVGGEALGR-LLVVYPWTQRFFESFGDLST
HBB_HORSE --------.Q.sG...a..L...D...-Ee.........-............d......N
HBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PTtKTYFPH
HBA_HORSE --------------VL..ADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PTtKTYFPH
MYG_PHYCA -------VlSEGEWqLVLHVWAKVeAd-.AGH.QdI.I.-.FKSh.E.LEK.dR.KH.K.
GLB5_PETMA PIVDTGSVAP.sAA..tKiRsA.AP.YSTY.TS.VDiLVKFFTST.AA.E..PK.KG.t.
LGB2_LUPLU --------GA..ESqAaL.KsS.EeF.ANIPKHTHRFFILv.EiA.AAkDL.SFLKGT.E
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
60 70 80 90 100 110
----:----|----:----|----:----|----:----|----:--..--|----:---
HBB_HUMAN PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH--VDPENFRLLGN
HBB_HORSE .G................Hs.Ge.vH..........A..........--...........
HBA_HUMAN F.LSH.sAq..G.....AD.LtnAv..v.dmPNALsA..d..AH..R--...V..k..Sh
HBA_HORSE F.LSH.sAq........GD.LtLAvG...d.P.ALsN..d..AH..R--...V..k..Sh
MYG_PHYCA EAEmKAsEDl.K..VT..T.LGAI.KKKGhHeAELKP.aqS.AT.HK--iPIkYLEFiSE
GLB5_PETMA A.QlKKsAD.rW.AeriiN.Vn.Av.Sm.dTeKMSMK.Rd.SGKHAK--SFQVdPqYFKV
LGB2_LUPLU VPQNNPELqAH.GKVFK.VYEaAIQLQvTGvVV.D...KN.GSVHvSKG.ADAh.PvvKE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
10 120 130 140
-|----:----|----:----|----:----|----:-....v.
HBB_HUMAN VLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
HBB_HORSE ...V...R....d...El..s.................------
HBA_HUMAN C.lVT..A.LPA....A.H.sLD.Fl.S.sTV.TS..R------
HBA_HORSE C.lST..V.LPNd...A.H.sLD.FlsS.sTV.TS..R------
MYG_PHYCA AiiH..HSRHPGd.GADA.G.MN.AlELFRKDi.A..KELGYQG
GLB5_PETMA lAAViADTVAAGdAGFEKLMsMICilLRS.Y-------------
LGB2_LUPLU AilKTiKEVV.AkwsEElNs.wTIAYDEl.IViKKeMnDAA---
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Output files for usage example 11
File: globins.showalign
10 20 30 40 50
...v....----:----|----:----.|----:----|.----:----|----:----|
HBB_HUMAN --------VHLTPEEksavtalwgkvn-vdevggealgr-llvvypwtqrffesfgdlst
HBB_HORSE --------.Q.SG...a..l...d...-ee.........-............d......n
HBA_HUMAN --------------Vl.padktnv.aa-wgk..ah.geygaealermfls.pttktyfph
HBA_HORSE --------------Vl..adktnv.aa-wsk...h.geygaealermflg.pttktyfph
MYG_PHYCA -------vLSEGEWQlvlhvwakvead-.agh.qdi.i.-.fksh.e.lek.dr.kh.k.
GLB5_PETMA pivdtgsvAP.SAA..tkirsa.ap.ysty.ts.vdilvkfftst.aa.e..pk.kg.t.
LGB2_LUPLU --------GA..ESQaal.kss.eef.anipkhthrffilv.eia.aakdl.sflkgt.e
60 70 80 90 100 110
----:----|----:----|----:----|----:----|----:--..--|----:---
HBB_HUMAN pdavmgnpkvkahgkkvlgafsdglahldnlkgtfatlselhcdklh--vdpenfrllgn
HBB_HORSE .g................hs.ge.vh..........a..........--...........
HBA_HUMAN f.lsh.saq..g.....ad.ltnav..v.dmpnalsa..d..ah..r--...v..k..sh
HBA_HORSE f.lsh.saq........gd.ltlavg...d.p.alsn..d..ah..r--...v..k..sh
MYG_PHYCA eaemkasedl.k..vt..t.lgai.kkkghheaelkp.aqs.at.hk--ipikylefise
GLB5_PETMA a.qlkksad.rw.aeriin.vn.av.sm.dtekmsmk.rd.sgkhak--sfqvdpqyfkv
LGB2_LUPLU vpqnnpelqah.gkvfk.vyeaaiqlqvtgvvv.d...kn.gsvhvskg.adah.pvvke
10 120 130 140
-|----:----|----:----|----:----|----:-....v.
HBB_HUMAN vlvcvlahhfgkeftppvqaayqkvvagvanalahkyh------
HBB_HORSE ...v...r....d...el..s.................------
HBA_HUMAN c.lvt..a.lpa....a.h.sld.fl.s.stv.ts..r------
HBA_HORSE c.lst..v.lpnd...a.h.sld.flss.stv.ts..r------
MYG_PHYCA aiih..hsrhpgd.gada.g.mn.alelfrkdi.a..kelgyqg
GLB5_PETMA laaviadtvaagdagfeklmsmicillrs.y-------------
LGB2_LUPLU ailktikevv.akwseelns.wtiaydel.ivikkemndaa---
Output files for usage example 12
File: globins.showalign
10 20 30 40 50 60
----:----|----:----|----:----|----:----|----:----|----:----|
GLB5_PETMA PIVDTGSVAP..AA.KtKiR.A.APVYSTY.TS.VDiLVKFFTST.AA.E..PK.KG.tT
HBA_HORSE --------------VL.AADKTNV.AA-WSk...H.GEYGAEAlERMFLG.PT.KTYFPH
HBA_HUMAN --------------VL.PADKTNV.AA-WGk..AH.GEYGAEAlERMFLS.PT.KTYFPH
HBB_HORSE --------VQ..GE.KaA.LaL.D.V.-EE....E..GR-.LVvY.WT.R..Ds.GD..N
HBB_HUMAN --------VH.tPE.K.A.TaL.G.V.-VD....E..GR-.LVvY.WT.R..Es.GD..T
LGB2_LUPLU --------GA.tESqAaL.K.S.EeF.ANIPKHTHRFFILvLE.A.AAkDL.SFLKGT.E
MYG_PHYCA -------VLSEGEWqLVLHVWAKVeAd-VAGH.QDI.IR-.FKSH.ETLEK.DR.KH.KT
Consensus xxxxxxxxxxLSxxExSxVxSxWxKxNxxxEVGGxALxxxLxxIxPxxQxFFxTFxxLSx
70 80 90 100 110 120
----:----|----:----|----:----|----:----|----:----|----:----|
GLB5_PETMA A.QlKK.AD.rW.AeriiN.vN.A.ASm..T.KMSMK.R..SGKHAk--SFQVdPqYFKV
HBA_HORSE F.LSH..A...A.....GD..TLA.G.....PGALsN......H...--...V.....S.
HBA_HUMAN F.LSH..A...G.....AD..TnA.A.v..mPNALsA......H...--...V.....S.
HBB_HORSE PGAvM.nPk..A......HsFGeG.H...n.kGTF.A..e..CD..H--...E..r..Gn
HBB_HUMAN P.AvM.nPk..A......G.FS.GlA...n.kGTF.T..e..CD..H--...E..r..Gn
LGB2_LUPLU VPQNNPEL.AHAGKVFK.VYEAAIQLQvTGvVVTD.T.Kn.GsVHvSKG.ADAh.PvvKE
MYG_PHYCA EAE.KA.EDl.K..VT..T..GAIlKKKGHH.AELKP.aQS..T.Hk--iPIKYLeFiSE
Consensus xDxMxGSxQVKxHGKKVLxALxDxVxHLDDLExxxAxLSDLHAxKLRxxVDPxNFKLLxH
130 140 150 160
----:----|----:----|----:----|----:----|----
GLB5_PETMA LAAViADTVAAG.AGF.KLM..ICI.LRS.Y-------------
HBA_HORSE C..ST..V.LPN....A.H..lD.F.sS.sTV.TS..R------
HBA_HUMAN C..VT..A.LPAe...A.H..lD.F..S.sTV.TS..R------
HBB_HORSE V.vV...R.FGK.....lQ..YQ.Vv.G..NA.AH..H------
HBB_HUMAN V.vC...H.FGKe...P.Q.aYQ.Vv.G..NA.AH..H------
LGB2_LUPLU Ai.KTiKEVVGAKwsE.lNsaWTIAYDEl.IViKKeMNDAA---
MYG_PHYCA AiiH..HSRHPG..GAdAQGa.N.A.ELFRKDiAA..KELGYQG
Consensus xLLxVLAxHxxxDFTPEVxASMxKxLAxVAxxLxxKYxx-xxxx
Data files
showalign reads in scoring matrices to determine the consensus 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
showalign reads in a scoring matrix to determine the consensus sequence
and to determine which matches are similar or not.
By using the -show option, the displayed sequences can 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)
Changing the similar matches to lowercase can optionally be disabled by
using the option -nosimilarcase.
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
The consensus line can be displayed in a mixture of uppercase and
lowercase symbols. Uppercase indicates a strong consensus and lowercase
a weak one. The cutoff for setting the consensus case is set by the
qualifier -setcase. If the number of residues at that position that
match the consensus value is greater than this, then the symbol is in
uppercase, otherwise the symbol is in lowercase. By default, the value
of -setcase is set so that if there are more than 50% of residues
identical to the consensus at that position, then the consensus is in
uppercase. To put all of the consensus symbols into uppercase or
lowercase, make -setcase zero or very large (try 100000 ?).
Other display options include Sequence numbering 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.
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 Display the trace in an ABI sequencer file
coderet Extract CDS, mRNA and translations from feature tables
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
entret Retrieve sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
infoalign Display basic information about a multiple sequence alignment
infoseq Display basic information about sequences
plotcon Plot conservation of a sequence alignment
prettyplot Draw a sequence alignment with pretty formatting
refseqget Get reference sequence
seqxref Retrieve all database cross-references for a sequence entry
seqxrefget Retrieve all cross-referenced data for a sequence entry
tranalign Generate an alignment of nucleic coding regions from aligned
proteins
variationget Get sequence variations
whichdb Search all sequence databases for an entry and retrieve it
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
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
None
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