
                             EMBOSS: infoalign
     _________________________________________________________________
   
                               Program 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

   Display only the name and sequence length of a sequence
% infoalign globin.seq -only -name -seqlength

   Display only the name, number of gap characters and differences to the
   consensus sequence
% infoalign globin.seq -only -name -gapcount -diffcount

   Display the name and number of gaps within a sequence
% infoalign globin.seq -only -name -gaps

   Display information formatted with HTML
% infoalign globin.seq -html

   Use the first sequence as the reference sequence to compare to
% infoalign globin.seq -refseq 1

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.

   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     Similarity scoring Matrix file
   -outfile            outfile    If you enter the name of a file here then
                                  this program will write the sequence details
                                  into that file.
   -html               bool       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               bool       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            bool       Display column headings
   -usa                bool       Display the USA of the sequence
   -name               bool       Display 'name' column
   -seqlength          bool       Display 'seqlength' column
   -alignlength        bool       Display 'alignlength' column
   -gaps               bool       Display number of gaps
   -gapcount           bool       Display number of gap positions
   -idcount            bool       Display number of identical positions
   -simcount           bool       Display number of similar positions
   -diffcount          bool       Display number of different positions
   -change             bool       Display % number of changed positions
   -description        bool       Display 'description' column

   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
   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 Similarity scoring Matrix file Comparison matrix file in
   EMBOSS data path EBLOSUM62 for protein
   EDNAFULL for DNA
   -outfile If you enter the name of a file here then this program will
   write the sequence details into that file. Output file stdout
   -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

   The output is displayed on the screen (stdout) by default. 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:
   
     * The USA (Uniform Sequence Address) that EMBOSS can use to read in
       the sequence.
     * Name - name of the sequence.
     * SeqLen - length of the sequence when all gap characters are
       removed.
     * AlignLen - length of the sequence including internal gap
       characters i.e. gaps at the start or the end are not included.
     * Gaps - number of gaps e.g. 'AAA---AAA' is 1 gap (and 3 gap
       characters long (see GapLen)).
     * GapLen - total number of internal gap characters, see the 3 gap
       characters above. This is the sum total of all of the internal gap
       characters in this sequence.
     * Ident - number of characters that are identical to the specified
       reference sequence (uppercase 'A' is identical to lowercase 'a').
     * Similar - number of characters which are non-identical - which
       score > 0 in the comparison matrix when compared to the reference
       sequence, but which are not identical.
     * Different - number of characters which score <= 0 in the
       comparison matrix when compared to the reference sequence.
     * %Change - a simple measure of the percentage change as compared to
       the reference sequence: (GapLen - Ident) * 100 / GapLen.
     * Description - the description annotation of teh sequence (if any).
       
   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:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata
       
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 name Description
   emma Multiple alignment program - interface to ClustalW program
   infoseq Displays some simple information about sequences
   plotcon Plots the quality of conservation of a sequence alignment
   prettyplot Displays aligned sequences, with colouring and boxing
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   tfm Displays a program's help documentation manual
   tranalign Align nucleic coding regions given the aligned proteins
   whichdb Search all databases for an entry
   wossname Finds 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.
   
Comments
