                                  infoalign



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Function

   Display basic information about a multiple sequence alignment

Description

   infoalign displays on screen basic information about sequences in an
   input multiple sequence alignment. This includes 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. Any
   combination of these records is easily selected or unselected for
   display. The same information may be written to an output file which
   (optionally) may be formatted in an HTML table.

   The reference sequence is the one against which all the other sequences
   are compared using a specified substitution matrix. It is either the
   calculated consensus sequence of the alignment (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 name. There are
   various options to control how the consensus is calculated.

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
Display basic information about 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
Display basic information about 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
Display basic information about 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
Display basic information about 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
Display basic information about 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
Display basic information about 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
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:


   Go to the output files for this example

   Example 8


% infoalign -auto @eclac.list -out test.out


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

   Example 9


% infoalign -auto tembl:v00296 -out test.out


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

Command line arguments

Display basic information about a multiple sequence alignment
Version: EMBOSS:6.6.0.0

   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)
   -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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit


Input file format

   infoalign reads a normal multiple sequence alignment file, as produced
   by a alignment program.

  Input files for usage example

  File: 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: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           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

  File: eclac.list

#Formerly ECLAC
tembl:J01636

#Formerly ECLACA
tembl:X51872

#Formerly ECLACI
tembl:V00294

#Formerly ECLACY
tembl:V00295

#Formerly ECLACZ
tembl:V00296

  Input files for usage example 9

   'tembl:v00296' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:v00296

ID   V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP.
XX
AC   V00296;
XX
DT   13-JUL-1983 (Rel. 03, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 5)
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; Gammaproteobacteria; Enterobacteriales;
OC   Enterobacteriaceae; Escherichia.
XX
RN   [1]
RP   1-3078
RX   PUBMED; 6313347.
RA   Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT   "Sequence of the lacZ gene of Escherichia coli";
RL   EMBO J. 2(4):593-597(1983).
XX
RN   [2]
RX   PUBMED; 3038536.
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(6):1809-1815(1987).
XX
CC   Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..3078
FT                   /organism="Escherichia coli"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:562"
FT   CDS             <1..3072
FT                   /transl_table=11
FT                   /note="galactosidase"
FT                   /db_xref="GOA:P00722"
FT                   /db_xref="InterPro:IPR004199"
FT                   /db_xref="InterPro:IPR006101"
FT                   /db_xref="InterPro:IPR006102"
FT                   /db_xref="InterPro:IPR006103"
FT                   /db_xref="InterPro:IPR006104"
FT                   /db_xref="InterPro:IPR008979"
FT                   /db_xref="InterPro:IPR011013"
FT                   /db_xref="InterPro:IPR013781"
FT                   /db_xref="InterPro:IPR013812"


  [Part of this file has been deleted for brevity]

     gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt       180
     gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag       240
     gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac       300
     accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg       360
     ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga       420
     attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt       480
     tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga       540
     gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag       600
     gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca       660
     caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg       720
     gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta       780
     tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat       840
     gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg       900
     tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc       960
     acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt      1020
     ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat      1080
     cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag      1140
     cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg      1200
     ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg      1260
     gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta      1320
     acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat      1380
     gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct      1440
     tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc      1500
     ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc      1560
     aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac      1620
     gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc      1680
     cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa      1740
     aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag      1800
     ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca      1860
     aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc      1920
     gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt      1980
     aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt      2040
     gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta      2100
     gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg      2160
     cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg      2220
     accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc      2280
     cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg      2340
     cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc      2400
     attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca      2460
     gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac      2520
     gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt      2580
     agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg      2640
     cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta      2700
     gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg      2760
     ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg      2820
     acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc      2880
     cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa      2940
     ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc      3000
     ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg      3060
     tgtcaaaaat aataataa                                                    3078
//

Output file format

  Output files for usage example

  File: globins.infoalign

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
msf::../../data/globins.msf:HBB_HUMAN   HBB_HUMAN     146       150     3
4       68      17      61      54.666668       0.610000
msf::../../data/globins.msf:HBB_HORSE   HBB_HORSE     146       150     3
4       68      17      61      54.666668       0.650000
msf::../../data/globins.msf:HBA_HUMAN   HBA_HUMAN     141       144     2
3       60      9       72      58.333332       0.650000
msf::../../data/globins.msf:HBA_HORSE   HBA_HORSE     141       144     2
3       63      6       72      56.250000       0.830000
msf::../../data/globins.msf:MYG_PHYCA   MYG_PHYCA     153       157     3
4       30      15      108     80.891716       1.000000
msf::../../data/globins.msf:GLB5_PETMA  GLB5_PETMA    149       151     1
2       32      16      101     78.807945       0.910000
msf::../../data/globins.msf:LGB2_LUPLU  LGB2_LUPLU    153       153     0
0       19      24      110     87.581696       0.430000

  Output files for usage example 2

  File: globins.infoalign

# Name        SeqLen    AlignLen        Gaps    GapLen  Ident   Similar Differ
% Change        Weight  Description
HBB_HUMAN     146       150     3       4       68      17      61      54.66666
8       0.610000
HBB_HORSE     146       150     3       4       68      17      61      54.66666
8       0.650000
HBA_HUMAN     141       144     2       3       60      9       72      58.33333
2       0.650000
HBA_HORSE     141       144     2       3       63      6       72      56.25000
0       0.830000
MYG_PHYCA     153       157     3       4       30      15      108     80.89171
6       1.000000
GLB5_PETMA    149       151     1       2       32      16      101     78.80794
5       0.910000
LGB2_LUPLU    153       153     0       0       19      24      110     87.58169
6       0.430000

  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 61
HBB_HORSE     4 61
HBA_HUMAN     3 72
HBA_HORSE     3 72
MYG_PHYCA     4 108
GLB5_PETMA    2 101
LGB2_LUPLU    0 110

  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>Weight</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>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.610000</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>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.650000</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>60</td>
<td>9</td>
<td>72</td>
<td>58.333332</td>
<td>0.650000</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>63</td>
<td>6</td>
<td>72</td>
<td>56.250000</td>
<td>0.830000</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>30</td>
<td>15</td>
<td>108</td>
<td>80.891716</td>
<td>1.000000</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>32</td>
<td>16</td>
<td>101</td>
<td>78.807945</td>
<td>0.910000</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>19</td>
<td>24</td>
<td>110</td>
<td>87.581696</td>
<td>0.430000</td>
<td></td>
</tr>
</table>

  Output files for usage example 7

  File: globins.infoalign

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
msf::../../data/globins.msf:HBB_HUMAN   HBB_HUMAN     146       150     3
4       146     0       0       2.666667        0.610000
msf::../../data/globins.msf:HBB_HORSE   HBB_HORSE     146       150     3
4       122     10      14      18.666666       0.650000
msf::../../data/globins.msf:HBA_HUMAN   HBA_HUMAN     141       144     2
3       48      19      74      66.666664       0.650000
msf::../../data/globins.msf:HBA_HORSE   HBA_HORSE     141       144     2
3       51      18      72      64.583336       0.830000
msf::../../data/globins.msf:MYG_PHYCA   MYG_PHYCA     153       157     3
4       30      22      101     80.891716       1.000000
msf::../../data/globins.msf:GLB5_PETMA  GLB5_PETMA    149       151     1
2       24      27      98      84.105957       0.910000
msf::../../data/globins.msf:LGB2_LUPLU  LGB2_LUPLU    153       153     0
0       21      28      104     86.274513       0.430000

  Output files for usage example 8

  File: test.out

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
tembl-id:J01636   J01636        7477    7477    0       0       374     0
7103    94.997993       1.000000        E.coli lactose operon with lacI, lacZ, l
acY and lacA genes.
tembl-id:X51872   X51872        1832    1832    0       0       374     0
1458    79.585152       1.000000        Escherichia coli lacA gene for thiogalac
toside transacetylase
tembl-id:V00294   V00294        1113    1113    0       0       302     0
811     72.866127       1.000000        E. coli laci gene (codes for the lac rep
ressor).
tembl-id:V00295   V00295        1500    1500    0       0       336     0
1164    77.599998       1.000000        E. coli lacY gene (codes for lactose per
mease).
tembl-id:V00296   V00296        3078    3078    0       0       373     0
2705    87.881744       1.000000        E. coli gene lacZ coding for beta-galact
osidase (EC 3.2.1.23).

  Output files for usage example 9

  File: test.out

# USA             Name        SeqLen    AlignLen        Gaps    GapLen  Ident
Similar Differ  % Change        Weight  Description
tembl-id:V00296   V00296        3078    3078    0       0       3078    0
0       0.000000        1.000000        E. coli gene lacZ coding for beta-galact
osidase (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 the 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

   There are many qualifiers to control exactly what information on the
   sequence is output and how it is formatted. If you only want a few
   fields in the output file, the command line may be shortended by
   preceding the appropriate qualifier with -only. For example, 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.

   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.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   abiview          Display the trace in an ABI sequencer file
   coderet          Extract CDS, mRNA and translations from feature tables
   edialign         Local multiple alignment of sequences
   emma             Multiple sequence alignment (ClustalW wrapper)
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   infoseq          Display basic information about sequences
   plotcon          Plot conservation of a sequence alignment
   prettyplot       Draw a sequence alignment with pretty formatting
   refseqget        Get reference sequence
   seqxref          Retrieve all database cross-references for a sequence entry
   seqxrefget       Retrieve all cross-referenced data for a sequence entry
   showalign        Display a multiple sequence alignment in pretty format
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins
   variationget     Get sequence variations
   whichdb          Search all sequence databases for an entry and retrieve it

Author(s)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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

   None
