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:

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
Displays a multiple sequence alignment
Input sequence set: ~/align.pep   
Output file [align.showalign]:

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         boolean    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    boolean    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     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.
   -[no]consensus      boolean    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         boolean    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    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.
   -html               boolean    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                boolean    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 <sequence>.showalign
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 This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. Comparison matrix file in EMBOSS data path EBLOSUM62 for protein
EDNAFULL for DNA
-[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
-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 numeric 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:

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:

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
abiviewReads ABI file and display the trace
cirdnaDraws circular maps of DNA constructs
emmaMultiple alignment program - interface to ClustalW program
infoalignInformation on a multiple sequence alignment
lindnaDraws linear maps of DNA constructs
pepnetDisplays proteins as a helical net
pepwheelShows protein sequences as helices
plotconPlots the quality of conservation of a sequence alignment
prettyplotDisplays aligned sequences, with colouring and boxing
prettyseqOutput sequence with translated ranges
remapDisplay a sequence with restriction cut sites, translation etc
seealsoFinds programs sharing group names
showdbDisplays information on the currently available databases
showfeatShow features of a sequence
showseqDisplay a sequence with features, translation etc
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tranalignAlign 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