|   | infoalign | 
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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.
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' countThe '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'
| % 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
| 
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
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-sequence] (Parameter 1) | seqset | The sequence alignment to be displayed. | Readable set of sequences | Required | 
| [-outfile] (Parameter 2) | outfile | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | <*>.infoalign | 
| 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. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA | 
| -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. | Any string | 0 | 
| -html | boolean | Format output as an HTML table | Boolean value Yes/No | No | 
| 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. | Number from 0.000 to 100.000 | 50.0 | 
| -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. | Number from 0.000 to 100.000 | 0.0 | 
| -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 -noweight' to get only the sequence length output, you can specify '-only -seqlength' | Boolean value Yes/No | No | 
| -heading | boolean | Display column headings | Boolean value Yes/No | @(!$(only)) | 
| -usa | boolean | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) | 
| -name | boolean | Display 'name' column | Boolean value Yes/No | @(!$(only)) | 
| -seqlength | boolean | Display 'seqlength' column | Boolean value Yes/No | @(!$(only)) | 
| -alignlength | boolean | Display 'alignlength' column | Boolean value Yes/No | @(!$(only)) | 
| -gaps | boolean | Display number of gaps | Boolean value Yes/No | @(!$(only)) | 
| -gapcount | boolean | Display number of gap positions | Boolean value Yes/No | @(!$(only)) | 
| -idcount | boolean | Display number of identical positions | Boolean value Yes/No | @(!$(only)) | 
| -simcount | boolean | Display number of similar positions | Boolean value Yes/No | @(!$(only)) | 
| -diffcount | boolean | Display number of different positions | Boolean value Yes/No | @(!$(only)) | 
| -change | boolean | Display % number of changed positions | Boolean value Yes/No | @(!$(only)) | 
| -weight | boolean | Display 'weight' column | Boolean value Yes/No | @(!$(only)) | 
| -description | boolean | Display 'description' column | Boolean value Yes/No | @(!$(only)) | 
| Associated qualifiers | ||||
| "-sequence" associated seqset qualifiers | ||||
| -sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0 | 
| -send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0 | 
| -sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N | 
| -sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | 
| -snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N | 
| -sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N | 
| -slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N | 
| -supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N | 
| -scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N | 
| -squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N | 
| -sformat1 -sformat_sequence | string | Input sequence format | Any string | |
| -iquery1 -iquery_sequence | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0 | 
| -sdbname1 -sdbname_sequence | string | Database name | Any string | |
| -sid1 -sid_sequence | string | Entryname | Any string | |
| -ufo1 -ufo_sequence | string | UFO features | Any string | |
| -fformat1 -fformat_sequence | string | Features format | Any string | |
| -fopenfile1 -fopenfile_sequence | string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory2 -odirectory_outfile | string | Output directory | Any string | |
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
| 
!!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~~~
 | 
| #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ 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
//
 | 
| # 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 | 
| # Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description HBB_HUMAN 146 150 3 4 68 17 61 54.666668 0.610000 HBB_HORSE 146 150 3 4 68 17 61 54.666668 0.650000 HBA_HUMAN 141 144 2 3 60 9 72 58.333332 0.650000 HBA_HORSE 141 144 2 3 63 6 72 56.250000 0.830000 MYG_PHYCA 153 157 3 4 30 15 108 80.891716 1.000000 GLB5_PETMA 149 151 1 2 32 16 101 78.807945 0.910000 LGB2_LUPLU 153 153 0 0 19 24 110 87.581696 0.430000 | 
| HBB_HUMAN 146 HBB_HORSE 146 HBA_HUMAN 141 HBA_HORSE 141 MYG_PHYCA 153 GLB5_PETMA 149 LGB2_LUPLU 153 | 
| 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 | 
| HBB_HUMAN 3 HBB_HORSE 3 HBA_HUMAN 2 HBA_HORSE 2 MYG_PHYCA 3 GLB5_PETMA 1 LGB2_LUPLU 0 | 
| <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> | 
| # 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 | 
| # 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, lacY and lacA genes. tembl-id:X51872 X51872 1832 1832 0 0 374 0 1458 79.585152 1.000000 Escherichia coli lacA gene for thiogalactoside transacetylase tembl-id:V00294 V00294 1113 1113 0 0 302 0 811 72.866127 1.000000 E. coli laci gene (codes for the lac repressor). tembl-id:V00295 V00295 1500 1500 0 0 336 0 1164 77.599998 1.000000 E. coli lacY gene (codes for lactose permease). tembl-id:V00296 V00296 3078 3078 0 0 373 0 2705 87.881744 1.000000 E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23). | 
| # 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-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:
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.
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:
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.
| 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 | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.