infoalign

 

Function

Information on a multiple sequence alignment

Description

infoalign is small utility to list some simple properties of sequences in an alignment.

It will write a table containing one line per sequence. The information is written out in columns separated by space or TAB characters. The columns of data are: the sequences' USA, name, two measures of length, counts of gaps, and numbers of identical, similar and different residues or bases in this sequence when compared to a reference sequence, together with a simple statistic of the % change between the reference sequence and this sequence.

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.

Any combination of these types of information can be easily selected or unselected.

By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by any other EMBOSS program that can read in one or more sequence to be analysed.

Usage

Here is a sample session with infoalign:
% infoalign globin.seq

Don't display the USA of a sequence

% infoalign globin.seq -nousa -out stdout

Display only the name and sequence length of a sequence

% infoalign globin.seq -only -name -seqlength -out stdout

Display only the name, number of gap characters and differences to the consensus sequence

% infoalign globin.seq -only -name -gapcount -diffcount -out stdout

Display the name and number of gaps within a sequence

% infoalign globin.seq -only -name -gaps -out stdout

Display information formatted with HTML

% infoalign globin.seq -html -out stdout

Use the first sequence as the reference sequence to compare to

% infoalign globin.seq -refseq 1 -out stdout

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 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.
   -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.
   -html               boolean    Format output as an HTML table

   Advanced qualifiers:
   -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.
   -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.
   -only               boolean    This is a way of shortening the command line
                                  if you only want a few things to be
                                  displayed. Instead of specifying:
                                  '-nohead -nousa -noname -noalign -nogaps
                                  -nogapcount -nosimcount -noidcount
                                  -nodiffcount'
                                  to get only the sequence length output, you
                                  can specify
                                  '-only -seqlength'
   -heading            boolean    Display column headings
   -usa                boolean    Display the USA of the sequence
   -name               boolean    Display 'name' column
   -seqlength          boolean    Display 'seqlength' column
   -alignlength        boolean    Display 'alignlength' column
   -gaps               boolean    Display number of gaps
   -gapcount           boolean    Display number of gap positions
   -idcount            boolean    Display number of identical positions
   -simcount           boolean    Display number of similar positions
   -diffcount          boolean    Display number of different positions
   -change             boolean    Display % number of changed positions
   -description        boolean    Display 'description' column

   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>.infoalign
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 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
-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
-html Format output as an HTML table Yes/No No
Advanced qualifiers Allowed values Default
-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
-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
-only This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount' to get only the sequence length output, you can specify '-only -seqlength' Yes/No No
-heading Display column headings Yes/No @(!$(only))
-usa Display the USA of the sequence Yes/No @(!$(only))
-name Display 'name' column Yes/No @(!$(only))
-seqlength Display 'seqlength' column Yes/No @(!$(only))
-alignlength Display 'alignlength' column Yes/No @(!$(only))
-gaps Display number of gaps Yes/No @(!$(only))
-gapcount Display number of gap positions Yes/No @(!$(only))
-idcount Display number of identical positions Yes/No @(!$(only))
-simcount Display number of similar positions Yes/No @(!$(only))
-diffcount Display number of different positions Yes/No @(!$(only))
-change Display % number of changed positions Yes/No @(!$(only))
-description Display 'description' column Yes/No @(!$(only))

Input file format

A normal multiple sequence alignment file, as produced by an alignment program is read in.

Output file format

A typical output file is:
# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident  Similar  Differ  % Change        Description
fasta::globin.seq:HBB_MACFU     HBB_MACFU     147       148     1       1      134      3       10      8.843537
fasta::globin.seq:HBD_HUMAN     HBD_HUMAN     147       148     1       1      128      7       12      12.925170
fasta::globin.seq:HBB_RABIT     HBB_RABIT     147       148     1       1      131      7       9       10.884354
fasta::globin.seq:HBB_BOVIN     HBB_BOVIN     146       147     1       1      121      10      15      17.123287
fasta::globin.seq:HBB_LAMGL     HBB_LAMGL     151       152     1       1      122      11      18      19.205297
fasta::globin.seq:HBE_HUMAN     HBE_HUMAN     143       150     2       7      104      14      25      27.272728
fasta::globin.seq:HBE_RABIT     HBE_RABIT     147       148     1       1      113      16      18      23.129251

The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters:

If qualifiers to inhibit various columns of information are used, then the remaining columns of information are output in the same order as shown above, so if '-noseqlength' is used, the order of output is: usa, name, alignlength, gaps, gapcount, idcount, simcount, diffcount, change, description.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as and are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplier by the user.

The lines of output information are guaranteed not to have trailing white-space at the end.

Data files

infoalign 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:

Notes

By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by other EMBOSS programs using the list-file specification of '@filename'.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
emmaMultiple alignment program - interface to ClustalW program
infoseqDisplays some simple information about sequences
plotconPlots the quality of conservation of a sequence alignment
prettyplotDisplays aligned sequences, with colouring and boxing
seealsoFinds programs sharing group names
showalignDisplays a multiple sequence alignment
showdbDisplays information on the currently available databases
textsearchSearch sequence documentation text. SRS and Entrez are faster!
tfmDisplays a program's help documentation manual
tranalignAlign nucleic coding regions given the aligned proteins
whichdbSearch all databases for an entry
wossnameFinds programs by keywords in their one-line documentation

Author(s)

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

History

Written (June 2001) - Gary Williams

Target users

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

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