EMBOSS: infoalign manual

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

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

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	54.666668	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

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, 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).

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-galactosidase (EC 3.2.1.23).

The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters:

The USA (Uniform Sequence Address) that EMBOSS can use to read in the sequence.
Name - name of the sequence.
SeqLen - length of the sequence when all gap characters are removed.
AlignLen - length of the sequence including internal gap characters i.e. gaps at the start or the end are not included.
Gaps - number of gaps e.g. 'AAA---AAA' is 1 gap (and 3 gap characters long (see GapLen)).
GapLen - total number of internal gap characters, see the 3 gap characters above. This is the sum total of all of the internal gap characters in this sequence.
Ident - number of characters that are identical to the specified reference sequence (uppercase 'A' is identical to lowercase 'a').
Similar - number of characters which are non-identical - which score > 0 in the comparison matrix when compared to the reference sequence, but which are not identical.
Different - number of characters which score <= 0 in the comparison matrix when compared to the reference sequence.
%Change - a simple measure of the percentage change as compared to the reference sequence: (AlignLen - Ident) * 100 / AlignLen
Description - the description annotation of 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.

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

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

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: globins.msf

Input files for usage example 8

File: eclac.list

Input files for usage example 9

Database entry: tembl:v00296

Output file format

Output files for usage example

File: globins.infoalign

Output files for usage example 2

File: globins.infoalign

Output files for usage example 3

File: globins.infoalign

Output files for usage example 4

File: globins.infoalign

Output files for usage example 5

File: globins.infoalign

Output files for usage example 6

File: globins.infoalign

Output files for usage example 7

File: globins.infoalign

Output files for usage example 8

File: test.out

Output files for usage example 9

File: test.out

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments