EMBOSS: infoalign

| ## 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