![]() |
EMBOSS: showalign |
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:
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 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 ?).
% 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
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 |
|
N | ||||||||||
-order | Output order of the sequences |
|
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 |
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:
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:
An example highlight range file is:
Some examples of different optional output styles follows:
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:
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
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:
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).
# 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.
% 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.
% embossdata -showall
% embossdata -fetch -file Exxx.dat
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