infoalign.txt

emboss的linux版本的源代码

                                 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.

Algorithm

   The set of aligned sequences is read in.

   If the reference sequence is the consensus sequence (this is the
   default) then this is calculated. If the reference sequence is
   specified as an ordinal number, then the sequences are counted (from
   1) until the reference sequence is identified. If the reference
   sequence is specified by its name then the names of the sequences are
   compared to the specified name until the reference sequence is
   identified.

Foreach sequence:

  Find the position of the first residue or base which is not a gap character.

  Find the position of the last residue or base which is not a gap character.

  Foreach position from the first non-gap character to the last non-gap
character:

    if the position is a gap character, then

      increment the 'GapLen' count

      if this character is the start of a new gap, increment the 'Gaps' count

    else

      the character at this position of the sequence and in the
      reference sequence are now compared.

      if the sequence character and the reference character are identical
      (apart from case) then

        increment the 'Ident' count

      else if the similarity matrix score for the two characters is > 0
      (i.e.  if they are similar) then

        increment the 'Similar' count

      else

        increment the 'Different' count

  The 'SeqLen' length of the sequence is the number of non-gap characters
  in the sequence (i.e. 'Ident' + 'Similar' + 'Different')

  The 'AlignLen' length of the sequence is the length from the first
  non-gap character to the last non-gap character.  (i.e.  the number of
  bases or residues of the sequence plus the number of gap characters
  internal to the sequence.)

  The '%Change' value for the sequence is calculated as:

  ('AlignLen' - 'Ident') * 100 / 'AlignLen'

Usage

   Here is a sample session with infoalign


% infoalign globins.msf 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   This example doesn't display the USA of the sequence:


% infoalign globins.msf -nousa 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 3

   Display only the name and sequence length of a sequence:


% infoalign globins.msf -only -name -seqlength 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 4

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


% infoalign globins.msf -only -name -gapcount -diffcount 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 5

   Display the name and number of gaps within a sequence:


% infoalign globins.msf -only -name -gaps 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 6

   Display information formatted with HTML:


% infoalign globins.msf -html 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 7

   Use the first sequence as the reference sequence to compare to:


% infoalign globins.msf -refseq 1 
Information on a multiple sequence alignment
Output file [globins.infoalign]: 

   Go to the output files for this example

   Example 8


% infoalign -auto tembl:eclac* -out test.out 

   Go to the input files for this example
   Go to the output files for this example

   Example 9


% infoalign -auto tembl:eclacz -out test.out 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     The sequence alignment to be displayed.
  [-outfile]           outfile    [*.infoalign] If you enter the name of a
                                  file here then this program will write the
                                  sequence details into that file.

   Additional (Optional) qualifiers:
   -matrix             matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  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.
   -refseq             string     [0] 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)
   -html               boolean    [N] Format output as an HTML table

   Advanced (Unprompted) qualifiers:
   -plurality          float      [50.0] 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)
   -identity           float      [0.0] 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)
   -only               boolean    [N] 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 -noweight'
                                  to get only the sequence length output, you
                                  can specify
                                  '-only -seqlength'
   -heading            boolean    [@(!$(only))] Display column headings
   -usa                boolean    [@(!$(only))] Display the USA of the
                                  sequence
   -name               boolean    [@(!$(only))] Display 'name' column
   -seqlength          boolean    [@(!$(only))] Display 'seqlength' column
   -alignlength        boolean    [@(!$(only))] Display 'alignlength' column
   -gaps               boolean    [@(!$(only))] Display number of gaps
   -gapcount           boolean    [@(!$(only))] Display number of gap
                                  positions
   -idcount            boolean    [@(!$(only))] Display number of identical
                                  positions
   -simcount           boolean    [@(!$(only))] Display number of similar
                                  positions
   -diffcount          boolean    [@(!$(only))] Display number of different
                                  positions
   -change             boolean    [@(!$(only))] Display % number of changed
                                  positions
   -weight             boolean    [@(!$(only))] Display 'weight' column
   -description        boolean    [@(!$(only))] Display 'description' column

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages