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

   Advanced (Unprompted) 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

   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 deaths
   

   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) The sequence alignment to be displayed. Readable set of
   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
   Additional (Optional) qualifiers Allowed values Default
   -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
   -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
   -html Format output as an HTML table Boolean value Yes/No No
   Advanced (Unprompted) 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' Boolean value Yes/No No
   -heading Display column headings Boolean value Yes/No @(!$(only))
   -usa Display the USA of the sequence Boolean value Yes/No @(!$(only))
   -name Display 'name' column Boolean value Yes/No @(!$(only))
   -seqlength Display 'seqlength' column Boolean value Yes/No @(!$(only))
   -alignlength Display 'alignlength' column Boolean value Yes/No
   @(!$(only))
   -gaps Display number of gaps Boolean value Yes/No @(!$(only))
   -gapcount Display number of gap positions Boolean value Yes/No
   @(!$(only))
   -idcount Display number of identical positions Boolean value Yes/No
   @(!$(only))
   -simcount Display number of similar positions Boolean value Yes/No
   @(!$(only))
   -diffcount Display number of different positions Boolean value Yes/No
   @(!$(only))
   -change Display % number of changed positions Boolean value Yes/No
   @(!$(only))
   -description Display 'description' column Boolean value Yes/No
   @(!$(only))
   
Input file format

   infoalign reads a normal multiple sequence alignment file, as produced
   by a alignment program.
   
  Input files for usage example
  
  File: ../../data/globins.msf
  
!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.14
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.15
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.15
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.19
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 0.23
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.21
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.10

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~
   
  Input files for usage example 8
  
   'tembl:eclac*' is a sequence entry in the example nucleic acid
   database 'tembl'
   
  Input files for usage example 9
  
  Database entry: tembl:eclacz
  
ID   ECLACZ     standard; DNA; PRO; 3078 BP.
XX
AC   V00296;
XX
SV   V00296.1
XX
DT   13-JUL-1983 (Rel. 03, Created)
DT   06-MAR-1996 (Rel. 47, Last updated, Version 4)
XX
DE   E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW   galactosidase.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1-3078
RX   MEDLINE; 84028567.
RA   Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT   "Sequence of the lacZ gene of Escherichia coli";
RL   EMBO J. 2:593-597(1983).
XX
RN   [2]
RX   MEDLINE; 87275876.
RA   Zell R., Fritz H.J.;
RT   "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT   deamination of 5-methyl-cytosine residues";
RL   EMBO J. 6:1809-1815(1987).
XX
DR   SWISS-PROT; P00722; BGAL_ECOLI.
XX
CC   Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3078
FT                   /db_xref="taxon:562"
FT                   /organism="Escherichia coli"
FT   CDS             <1..3072
FT                   /db_xref="SWISS-PROT:P00722"
FT                   /note="galactosidase"
FT                   /transl_table=11
FT                   /protein_id="CAA23573.1"
FT                   /translation="TMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEART
D
FT                   RPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNV
T
FT                   YPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYG
Q
FT                   DSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQ
I
FT                   SDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIID
E


  [Part of this file has been deleted for brevity]

     gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt       18
0
     gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag       24
0
     gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac       30
0
     accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg       36
0
     ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga       42
0
     attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt       48
0
     tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga       54
0
     gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag       60
0
     gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca       66
0
     caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg       72
0
     gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta       78
0
     tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat       84
0
     gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg       90
0
     tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc       96
0
     acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt      102
0
     ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat      108
0
     cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag      114
0
     cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg      120
0
     ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg      126
0
     gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta      132
0
     acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat      138
0
     gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct      144
0
     tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc      150
0
     ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc      156
0
     aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac      162
0
     gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc      168
0
     cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa      174
0
     aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag      180
0
     ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca      186
0
     aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc      192
0
     gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt      198
0
     aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt      204
0
     gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta      210
0
     gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg      216
0
     cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg      222
0
     accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc      228
0
     cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg      234
0
     cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc      240
0
     attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca      246
0
     gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac      252
0
     gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt      258
0
     agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg      264
0
     cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta      270
0
     gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg      276
0
     ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg      282
0
     acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc      288
0
     cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa      294
0
     ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc      300
0
     ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg      306
0
     tgtcaaaaat aataataa                                                    307
8
//
   
Output file format

  Output files for usage example
  
  File: globins.infoalign
  
# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Description
msf::../../data/globins.msf:HBB_HUMAN   HBB_HUMAN     146       150     3
4       48      10      88      68.000000
msf::../../data/globins.msf:HBB_HORSE   HBB_HORSE     146       150     3
4       48      10      88      68.000000
msf::../../data/globins.msf:HBA_HUMAN   HBA_HUMAN     141       144     2
3       45      7       89      68.750000
msf::../../data/globins.msf:HBA_HORSE   HBA_HORSE     141       144     2
3       48      4       89      66.666664
msf::../../data/globins.msf:MYG_PHYCA   MYG_PHYCA     153       157     3
4       25      13      115     84.076431
msf::../../data/globins.msf:GLB5_PETMA  GLB5_PETMA    149       151     1
2       21      13      115     86.092712
msf::../../data/globins.msf:LGB2_LUPLU  LGB2_LUPLU    153       153     0
0       11      20      122     92.810455
   
  Output files for usage example 2
  
  File: globins.infoalign
  
# Name        SeqLen    AlignLen        Gaps    GapLen  Ident   Similar Differ
% Change        Description
HBB_HUMAN     146       150     3       4       48      10      88      68.0000
00
HBB_HORSE     146       150     3       4       48      10      88      68.0000
00
HBA_HUMAN     141       144     2       3       45      7       89      68.7500
00
HBA_HORSE     141       144     2       3       48      4       89      66.6666
64
MYG_PHYCA     153       157     3       4       25      13      115     84.0764
31
GLB5_PETMA    149       151     1       2       21      13      115     86.0927
12
LGB2_LUPLU    153       153     0       0       11      20      122     92.8104
55
   
  Output files for usage example 3
  
  File: globins.infoalign
  
HBB_HUMAN     146
HBB_HORSE     146
HBA_HUMAN     141
HBA_HORSE     141
MYG_PHYCA     153
GLB5_PETMA    149
LGB2_LUPLU    153
   
  Output files for usage example 4
  
  File: globins.infoalign
  
HBB_HUMAN     4 88
HBB_HORSE     4 88
HBA_HUMAN     3 89
HBA_HORSE     3 89
MYG_PHYCA     4 115
GLB5_PETMA    2 115
LGB2_LUPLU    0 122
   
  Output files for usage example 5
  
  File: globins.infoalign
  
HBB_HUMAN     3
HBB_HORSE     3
HBA_HUMAN     2
HBA_HORSE     2
MYG_PHYCA     3
GLB5_PETMA    1
LGB2_LUPLU    0
   
  Output files for usage example 6
  
  File: globins.infoalign
  
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>USA</th><th>Name</th><th>Sequence Length</th><th>Aligned Length</th><th
>Gaps</th><th>Gap Length</th><th>Identity</th><th>Similarity</th><th>Difference
</th><th>% Change</th><th>Description</th></tr>
<tr><td>msf::../../data/globins.msf:HBB_HUMAN</td>
<td>HBB_HUMAN</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>48</td>
<td>10</td>
<td>88</td>
<td>68.000000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBB_HORSE</td>
<td>HBB_HORSE</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>48</td>
<td>10</td>
<td>88</td>
<td>68.000000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HUMAN</td>
<td>HBA_HUMAN</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>45</td>
<td>7</td>
<td>89</td>
<td>68.750000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HORSE</td>
<td>HBA_HORSE</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>48</td>
<td>4</td>
<td>89</td>
<td>66.666664</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:MYG_PHYCA</td>
<td>MYG_PHYCA</td>
<td>153</td>
<td>157</td>
<td>3</td>
<td>4</td>
<td>25</td>
<td>13</td>
<td>115</td>
<td>84.076431</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:GLB5_PETMA</td>
<td>GLB5_PETMA</td>
<td>149</td>
<td>151</td>
<td>1</td>
<td>2</td>
<td>21</td>
<td>13</td>
<td>115</td>
<td>86.092712</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:LGB2_LUPLU</td>
<td>LGB2_LUPLU</td>
<td>153</td>
<td>153</td>
<td>0</td>
<td>0</td>
<td>11</td>
<td>20</td>
<td>122</td>
<td>92.810455</td>
<td></td>
</tr>
</table>
   
  Output files for usage example 7
  
  File: globins.infoalign
  
# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Description
msf::../../data/globins.msf:HBB_HUMAN   HBB_HUMAN     146       150     3
4       146     0       0       2.666667
msf::../../data/globins.msf:HBB_HORSE   HBB_HORSE     146       150     3
4       122     10      14      18.666666
msf::../../data/globins.msf:HBA_HUMAN   HBA_HUMAN     141       144     2
3       48      19      74      66.666664
msf::../../data/globins.msf:HBA_HORSE   HBA_HORSE     141       144     2
3       51      18      72      64.583336
msf::../../data/globins.msf:MYG_PHYCA   MYG_PHYCA     153       157     3
4       30      22      101     80.891716
msf::../../data/globins.msf:GLB5_PETMA  GLB5_PETMA    149       151     1
2       24      27      98      84.105957
msf::../../data/globins.msf:LGB2_LUPLU  LGB2_LUPLU    153       153     0
0       21      28      104     86.274513
   
  Output files for usage example 8
  
  File: test.out
  
# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Description
tembl-id:ECLAC    ECLAC         7477    7477    0       0       65      0
7412    99.130669       E.coli lactose operon with lacI, lacZ, lacY and lacA ge
nes.
tembl-id:ECLACA   ECLACA        1832    1832    0       0       71      0
1761    96.124451       Escherichia coli lacA gene for thiogalactoside transace
tylase
tembl-id:ECLACI   ECLACI        1113    1113    0       0       67      0
1046    93.980232       E. coli laci gene (codes for the lac repressor).
tembl-id:ECLACY   ECLACY        1500    1500    0       0       68      0
1432    95.466667       E. coli lacY gene (codes for lactose permease).
tembl-id:ECLACZ   ECLACZ        3078    3078    0       0       72      0
3006    97.660820       E. coli gene lacZ coding for beta-galactosidase (EC 3.2
.1.23).
   
  Output files for usage example 9
  
  File: test.out
  
# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Description
tembl-id:ECLACZ   ECLACZ        3078    3078    0       0       0       0
3078    100.000000      E. coli gene lacZ coding for beta-galactosidase (EC 3.2
.1.23).
   
   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: (AlignLen - Ident) * 100 / AlignLen
     * 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)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, 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
