| 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 ../../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

       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.

       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     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.
       -html               boolean    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               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" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-outfile" related 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 required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | The sequence alignment to be displayed. | Readable 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
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 | 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
-html | Format output as an HTML table | Boolean value 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' | 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="TMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTD
    FT                   RPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVT
    FT                   YPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQ
    FT                   DSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQI
    FT                   SDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDE

      [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	Description
    msf::../../data/globins.msf:HBB_HUMAN	HBB_HUMAN     150	154	3	4	48	10	92	68.000000
    msf::../../data/globins.msf:HBB_HORSE	HBB_HORSE     150	154	3	4	48	10	92	68.000000
    msf::../../data/globins.msf:HBA_HUMAN	HBA_HUMAN     144	147	2	3	45	7	92	68.750000
    msf::../../data/globins.msf:HBA_HORSE	HBA_HORSE     144	147	2	3	48	4	92	66.666664
    msf::../../data/globins.msf:MYG_PHYCA	MYG_PHYCA     157	161	3	4	25	13	119	84.076431
    msf::../../data/globins.msf:GLB5_PETMA	GLB5_PETMA    151	153	1	2	21	13	117	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     150	154	3	4	48	10	92	68.000000
    HBB_HORSE     150	154	3	4	48	10	92	68.000000
    HBA_HUMAN     144	147	2	3	45	7	92	68.750000
    HBA_HORSE     144	147	2	3	48	4	92	66.666664
    MYG_PHYCA     157	161	3	4	25	13	119	84.076431
    GLB5_PETMA    151	153	1	2	21	13	117	86.092712
    LGB2_LUPLU    153	153	0	0	11	20	122	92.810455

### Output files for usage example 3

### File: globins.infoalign

    HBB_HUMAN     150
    HBB_HORSE     150
    HBA_HUMAN     144
    HBA_HORSE     144
    MYG_PHYCA     157
    GLB5_PETMA    151
    LGB2_LUPLU    153

### Output files for usage example 4

### File: globins.infoalign

    HBB_HUMAN     4	92
    HBB_HORSE     4	92
    HBA_HUMAN     3	92
    HBA_HORSE     3	92
    MYG_PHYCA     4	119
    GLB5_PETMA    2	117
    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>150</td>
    <td>154</td>
    <td>3</td>
    <td>4</td>
    <td>48</td>
    <td>10</td>
    <td>92</td>
    <td>68.000000</td>
    <td></td>
    </tr>
    <tr><td>msf::../../data/globins.msf:HBB_HORSE</td>
    <td>HBB_HORSE</td>
    <td>150</td>
    <td>154</td>
    <td>3</td>
    <td>4</td>
    <td>48</td>
    <td>10</td>
    <td>92</td>
    <td>68.000000</td>
    <td></td>
    </tr>
    <tr><td>msf::../../data/globins.msf:HBA_HUMAN</td>
    <td>HBA_HUMAN</td>
    <td>144</td>
    <td>147</td>
    <td>2</td>
    <td>3</td>
    <td>45</td>
    <td>7</td>
    <td>92</td>
    <td>68.750000</td>
    <td></td>
    </tr>
    <tr><td>msf::../../data/globins.msf:HBA_HORSE</td>
    <td>HBA_HORSE</td>
    <td>144</td>
    <td>147</td>
    <td>2</td>
    <td>3</td>
    <td>48</td>
    <td>4</td>
    <td>92</td>
    <td>66.666664</td>
    <td></td>
    </tr>
    <tr><td>msf::../../data/globins.msf:MYG_PHYCA</td>
    <td>MYG_PHYCA</td>
    <td>157</td>
    <td>161</td>
    <td>3</td>
    <td>4</td>
    <td>25</td>
    <td>13</td>
    <td>119</td>
    <td>84.076431</td>
    <td></td>
    </tr>
    <tr><td>msf::../../data/globins.msf:GLB5_PETMA</td>
    <td>GLB5_PETMA</td>
    <td>151</td>
    <td>153</td>
    <td>1</td>
    <td>2</td>
    <td>21</td>
    <td>13</td>
    <td>117</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     150	154	3	4	150	0	0	0.000000
    msf::../../data/globins.msf:HBB_HORSE	HBB_HORSE     150	154	3	4	126	10	14	16.000000
    msf::../../data/globins.msf:HBA_HUMAN	HBA_HUMAN     144	147	2	3	51	19	74	64.583336
    msf::../../data/globins.msf:HBA_HORSE	HBA_HORSE     144	147	2	3	54	18	72	62.500000
    msf::../../data/globins.msf:MYG_PHYCA	MYG_PHYCA     157	161	3	4	34	22	101	78.343948
    msf::../../data/globins.msf:GLB5_PETMA	GLB5_PETMA    151	153	1	2	26	27	98	82.781456
    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 genes.
    tembl-id:ECLACA   ECLACA        1832	1832	0	0	71	0	1761	96.124451	Escherichia coli lacA gene for thiogalactoside transacetylase
    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: (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)

Gary Williams (gwilliam © hgmp.mrc.ac.uk)
HGMP-RC, 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