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|
infoalign
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
Function
Display basic information about a multiple sequence alignment
Description
infoalign displays on screen basic information about sequences in an
input multiple sequence alignment. This includes the sequences' USA,
name, two measures of length, counts of gaps, and numbers of identical,
similar and different residues or bases in this sequence when compared
to a reference sequence, together with a simple statistic of the %
change between the reference sequence and this sequence. Any
combination of these records is easily selected or unselected for
display. The same information may be written to an output file which
(optionally) may be formatted in an HTML table.
The reference sequence is the one against which all the other sequences
are compared using a specified substitution matrix. It is either the
calculated consensus sequence of the alignment (the default) or it can
be one of the set of aligned sequences, specified by either the ordinal
number of that sequence in the input file, or by name. There are
various options to control how the consensus is calculated.
Algorithm
The set of aligned sequences is read in.
If the reference sequence is the consensus sequence (this is the
default) then this is calculated. If the reference sequence is
specified as an ordinal number, then the sequences are counted (from 1)
until the reference sequence is identified. If the reference sequence
is specified by its name then the names of the sequences are compared
to the specified name until the reference sequence is identified.
Foreach sequence:
Find the position of the first residue or base which is not a gap character.
Find the position of the last residue or base which is not a gap character.
Foreach position from the first non-gap character to the last non-gap
character:
if the position is a gap character, then
increment the 'GapLen' count
if this character is the start of a new gap, increment the 'Gaps' count
else
the character at this position of the sequence and in the
reference sequence are now compared.
if the sequence character and the reference character are identical
(apart from case) then
increment the 'Ident' count
else if the similarity matrix score for the two characters is > 0
(i.e. if they are similar) then
increment the 'Similar' count
else
increment the 'Different' count
The 'SeqLen' length of the sequence is the number of non-gap characters
in the sequence (i.e. 'Ident' + 'Similar' + 'Different')
The 'AlignLen' length of the sequence is the length from the first
non-gap character to the last non-gap character. (i.e. the number of
bases or residues of the sequence plus the number of gap characters
internal to the sequence.)
The '%Change' value for the sequence is calculated as:
('AlignLen' - 'Ident') * 100 / 'AlignLen'
Usage
Here is a sample session with infoalign
% infoalign globins.msf
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the input files for this example
Go to the output files for this example
Example 2
This example doesn't display the USA of the sequence:
% infoalign globins.msf -nousa
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 3
Display only the name and sequence length of a sequence:
% infoalign globins.msf -only -name -seqlength
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 4
Display only the name, number of gap characters and differences to the
consensus sequence:
% infoalign globins.msf -only -name -gapcount -diffcount
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 5
Display the name and number of gaps within a sequence:
% infoalign globins.msf -only -name -gaps
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 6
Display information formatted with HTML:
% infoalign globins.msf -html
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 7
Use the first sequence as the reference sequence to compare to:
% infoalign globins.msf -refseq 1
Display basic information about a multiple sequence alignment
Output file [globins.infoalign]:
Go to the output files for this example
Example 8
% infoalign -auto @eclac.list -out test.out
Go to the input files for this example
Go to the output files for this example
Example 9
% infoalign -auto tembl:v00296 -out test.out
Go to the input files for this example
Go to the output files for this example
Command line arguments
Display basic information about a multiple sequence alignment
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqset The sequence alignment to be displayed.
[-outfile] outfile [*.infoalign] If you enter the name of a
file here then this program will write the
sequence details into that file.
Additional (Optional) qualifiers:
-matrix matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-refseq string [0] If you give the number in the alignment
or the name of a sequence, it will be taken
to be the reference sequence. The reference
sequence is the one against which all the
other sequences are compared. If this is set
to 0 then the consensus sequence will be
used as the reference sequence. By default
the consensus sequence is used as the
reference sequence. (Any string)
-html boolean [N] Format output as an HTML table
Advanced (Unprompted) qualifiers:
-plurality float [50.0] Set a cut-off for the % of positive
scoring matches below which there is no
consensus. The default plurality is taken as
50% of the total weight of all the
sequences in the alignment. (Number from
0.000 to 100.000)
-identity float [0.0] Provides the facility of setting the
required number of identities at a position
for it to give a consensus. Therefore, if
this is set to 100% only columns of
identities contribute to the consensus.
(Number from 0.000 to 100.000)
-only boolean [N] This is a way of shortening the command
line if you only want a few things to be
displayed. Instead of specifying:
'-nohead -nousa -noname -noalign -nogaps
-nogapcount -nosimcount -noidcount
-nodiffcount -noweight'
to get only the sequence length output, you
can specify
'-only -seqlength'
-heading boolean [@(!$(only))] Display column headings
-usa boolean [@(!$(only))] Display the USA of the
sequence
-name boolean [@(!$(only))] Display 'name' column
-seqlength boolean [@(!$(only))] Display 'seqlength' column
-alignlength boolean [@(!$(only))] Display 'alignlength' column
-gaps boolean [@(!$(only))] Display number of gaps
-gapcount boolean [@(!$(only))] Display number of gap
positions
-idcount boolean [@(!$(only))] Display number of identical
positions
-simcount boolean [@(!$(only))] Display number of similar
positions
-diffcount boolean [@(!$(only))] Display number of different
positions
-change boolean [@(!$(only))] Display % number of changed
positions
-weight boolean [@(!$(only))] Display 'weight' column
-description boolean [@(!$(only))] Display 'description' column
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
Input file format
infoalign reads a normal multiple sequence alignment file, as produced
by a alignment program.
Input files for usage example
File: globins.msf
!!AA_MULTIPLE_ALIGNMENT 1.0
../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 ..
Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.61
Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.65
Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.65
Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.83
Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 1.00
Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.91
Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.43
//
1 50
HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD
51 100
HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN
101 150
HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA
151 164
HBB_HUMAN NALAHKYH~~~~~~
HBB_HORSE NALAHKYH~~~~~~
HBA_HUMAN TVLTSKYR~~~~~~
HBA_HORSE TVLTSKYR~~~~~~
MYG_PHYCA KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~
Input files for usage example 8
File: eclac.list
#Formerly ECLAC
tembl:J01636
#Formerly ECLACA
tembl:X51872
#Formerly ECLACI
tembl:V00294
#Formerly ECLACY
tembl:V00295
#Formerly ECLACZ
tembl:V00296
Input files for usage example 9
'tembl:v00296' is a sequence entry in the example nucleic acid database
'tembl'
Database entry: tembl:v00296
ID V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP.
XX
AC V00296;
XX
DT 13-JUL-1983 (Rel. 03, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 5)
XX
DE E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW galactosidase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1-3078
RX PUBMED; 6313347.
RA Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT "Sequence of the lacZ gene of Escherichia coli";
RL EMBO J. 2(4):593-597(1983).
XX
RN [2]
RX PUBMED; 3038536.
RA Zell R., Fritz H.J.;
RT "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT deamination of 5-methyl-cytosine residues";
RL EMBO J. 6(6):1809-1815(1987).
XX
CC Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH Key Location/Qualifiers
FH
FT source 1..3078
FT /organism="Escherichia coli"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:562"
FT CDS <1..3072
FT /transl_table=11
FT /note="galactosidase"
FT /db_xref="GOA:P00722"
FT /db_xref="InterPro:IPR004199"
FT /db_xref="InterPro:IPR006101"
FT /db_xref="InterPro:IPR006102"
FT /db_xref="InterPro:IPR006103"
FT /db_xref="InterPro:IPR006104"
FT /db_xref="InterPro:IPR008979"
FT /db_xref="InterPro:IPR011013"
FT /db_xref="InterPro:IPR013781"
FT /db_xref="InterPro:IPR013812"
[Part of this file has been deleted for brevity]
gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt 180
gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag 240
gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac 300
accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg 360
ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga 420
attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt 480
tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga 540
gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag 600
gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca 660
caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg 720
gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta 780
tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat 840
gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg 900
tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc 960
acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt 1020
ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat 1080
cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag 1140
cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg 1200
ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg 1260
gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta 1320
acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat 1380
gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct 1440
tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc 1500
ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc 1560
aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac 1620
gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc 1680
cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa 1740
aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag 1800
ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca 1860
aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc 1920
gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt 1980
aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt 2040
gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta 2100
gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg 2160
cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg 2220
accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc 2280
cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg 2340
cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc 2400
attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca 2460
gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac 2520
gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt 2580
agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg 2640
cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta 2700
gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg 2760
ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg 2820
acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc 2880
cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa 2940
ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc 3000
ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg 3060
tgtcaaaaat aataataa 3078
//
Output file format
Output files for usage example
File: globins.infoalign
# USA Name SeqLen AlignLen Gaps GapLen Ident
Similar Differ % Change Weight Description
msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3
4 68 17 61 54.666668 0.610000
msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3
4 68 17 61 54.666668 0.650000
msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2
3 60 9 72 58.333332 0.650000
msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2
3 63 6 72 56.250000 0.830000
msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3
4 30 15 108 80.891716 1.000000
msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1
2 32 16 101 78.807945 0.910000
msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0
0 19 24 110 87.581696 0.430000
Output files for usage example 2
File: globins.infoalign
# Name SeqLen AlignLen Gaps GapLen Ident Similar Differ
% Change Weight Description
HBB_HUMAN 146 150 3 4 68 17 61 54.66666
8 0.610000
HBB_HORSE 146 150 3 4 68 17 61 54.66666
8 0.650000
HBA_HUMAN 141 144 2 3 60 9 72 58.33333
2 0.650000
HBA_HORSE 141 144 2 3 63 6 72 56.25000
0 0.830000
MYG_PHYCA 153 157 3 4 30 15 108 80.89171
6 1.000000
GLB5_PETMA 149 151 1 2 32 16 101 78.80794
5 0.910000
LGB2_LUPLU 153 153 0 0 19 24 110 87.58169
6 0.430000
Output files for usage example 3
File: globins.infoalign
HBB_HUMAN 146
HBB_HORSE 146
HBA_HUMAN 141
HBA_HORSE 141
MYG_PHYCA 153
GLB5_PETMA 149
LGB2_LUPLU 153
Output files for usage example 4
File: globins.infoalign
HBB_HUMAN 4 61
HBB_HORSE 4 61
HBA_HUMAN 3 72
HBA_HORSE 3 72
MYG_PHYCA 4 108
GLB5_PETMA 2 101
LGB2_LUPLU 0 110
Output files for usage example 5
File: globins.infoalign
HBB_HUMAN 3
HBB_HORSE 3
HBA_HUMAN 2
HBA_HORSE 2
MYG_PHYCA 3
GLB5_PETMA 1
LGB2_LUPLU 0
Output files for usage example 6
File: globins.infoalign
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>USA</th><th>Name</th><th>Sequence Length</th><th>Aligned Length</th><th>
Gaps</th><th>Gap Length</th><th>Identity</th><th>Similarity</th><th>Difference</
th><th>% Change</th><th>Weight</th><th>Description</th></tr>
<tr><td>msf::../../data/globins.msf:HBB_HUMAN</td>
<td>HBB_HUMAN</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.610000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBB_HORSE</td>
<td>HBB_HORSE</td>
<td>146</td>
<td>150</td>
<td>3</td>
<td>4</td>
<td>68</td>
<td>17</td>
<td>61</td>
<td>54.666668</td>
<td>0.650000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HUMAN</td>
<td>HBA_HUMAN</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>60</td>
<td>9</td>
<td>72</td>
<td>58.333332</td>
<td>0.650000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:HBA_HORSE</td>
<td>HBA_HORSE</td>
<td>141</td>
<td>144</td>
<td>2</td>
<td>3</td>
<td>63</td>
<td>6</td>
<td>72</td>
<td>56.250000</td>
<td>0.830000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:MYG_PHYCA</td>
<td>MYG_PHYCA</td>
<td>153</td>
<td>157</td>
<td>3</td>
<td>4</td>
<td>30</td>
<td>15</td>
<td>108</td>
<td>80.891716</td>
<td>1.000000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:GLB5_PETMA</td>
<td>GLB5_PETMA</td>
<td>149</td>
<td>151</td>
<td>1</td>
<td>2</td>
<td>32</td>
<td>16</td>
<td>101</td>
<td>78.807945</td>
<td>0.910000</td>
<td></td>
</tr>
<tr><td>msf::../../data/globins.msf:LGB2_LUPLU</td>
<td>LGB2_LUPLU</td>
<td>153</td>
<td>153</td>
<td>0</td>
<td>0</td>
<td>19</td>
<td>24</td>
<td>110</td>
<td>87.581696</td>
<td>0.430000</td>
<td></td>
</tr>
</table>
Output files for usage example 7
File: globins.infoalign
# USA Name SeqLen AlignLen Gaps GapLen Ident
Similar Differ % Change Weight Description
msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3
4 146 0 0 2.666667 0.610000
msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3
4 122 10 14 18.666666 0.650000
msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2
3 48 19 74 66.666664 0.650000
msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2
3 51 18 72 64.583336 0.830000
msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3
4 30 22 101 80.891716 1.000000
msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1
2 24 27 98 84.105957 0.910000
msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0
0 21 28 104 86.274513 0.430000
Output files for usage example 8
File: test.out
# USA Name SeqLen AlignLen Gaps GapLen Ident
Similar Differ % Change Weight Description
tembl-id:J01636 J01636 7477 7477 0 0 374 0
7103 94.997993 1.000000 E.coli lactose operon with lacI, lacZ, l
acY and lacA genes.
tembl-id:X51872 X51872 1832 1832 0 0 374 0
1458 79.585152 1.000000 Escherichia coli lacA gene for thiogalac
toside transacetylase
tembl-id:V00294 V00294 1113 1113 0 0 302 0
811 72.866127 1.000000 E. coli laci gene (codes for the lac rep
ressor).
tembl-id:V00295 V00295 1500 1500 0 0 336 0
1164 77.599998 1.000000 E. coli lacY gene (codes for lactose per
mease).
tembl-id:V00296 V00296 3078 3078 0 0 373 0
2705 87.881744 1.000000 E. coli gene lacZ coding for beta-galact
osidase (EC 3.2.1.23).
Output files for usage example 9
File: test.out
# USA Name SeqLen AlignLen Gaps GapLen Ident
Similar Differ % Change Weight Description
tembl-id:V00296 V00296 3078 3078 0 0 3078 0
0 0.000000 1.000000 E. coli gene lacZ coding for beta-galact
osidase (EC 3.2.1.23).
The first non-blank line is the heading. This is followed by one line
per sequence containing the following columns of data separated by one
of more space or TAB characters:
* The USA (Uniform Sequence Address) that EMBOSS can use to read in
the sequence.
* Name - name of the sequence.
* SeqLen - length of the sequence when all gap characters are
removed.
* AlignLen - length of the sequence including internal gap characters
i.e. gaps at the start or the end are not included.
* Gaps - number of gaps e.g. 'AAA---AAA' is 1 gap (and 3 gap
characters long (see GapLen)).
* GapLen - total number of internal gap characters, see the 3 gap
characters above. This is the sum total of all of the internal gap
characters in this sequence.
* Ident - number of characters that are identical to the specified
reference sequence (uppercase 'A' is identical to lowercase 'a').
* Similar - number of characters which are non-identical - which
score > 0 in the comparison matrix when compared to the reference
sequence, but which are not identical.
* Different - number of characters which score <= 0 in the comparison
matrix when compared to the reference sequence.
* %Change - a simple measure of the percentage change as compared to
the reference sequence: (AlignLen - Ident) * 100 / AlignLen
* Description - the description annotation of the sequence (if any).
If qualifiers to inhibit various columns of information are used, then
the remaining columns of information are output in the same order as
shown above, so if '-noseqlength' is used, the order of output is: usa,
name, alignlength, gaps, gapcount, idcount, simcount, diffcount,
change, description.
When the -html qualifier is specified, then the output will be wrapped
in HTML tags, ready for inclusion in a Web page. Note that tags such as
and are not output by this program as the table of databases is
expected to form only part of the contents of a web page - the rest of
the web page must be supplier by the user.
The lines of output information are guaranteed not to have trailing
white-space at the end.
Data files
infoalign reads in scoring matrices to determine the consensus sequence
and to determine which matches are similar or not.
EMBOSS data files are distributed with the application and stored in
the standard EMBOSS data directory, which is defined by the EMBOSS
environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called ".embossdata". Files
for all EMBOSS runs can be put in the user's home directory, or again
in a subdirectory called ".embossdata".
The directories are searched in the following order:
* . (your current directory)
* .embossdata (under your current directory)
* ~/ (your home directory)
* ~/.embossdata
Notes
There are many qualifiers to control exactly what information on the
sequence is output and how it is formatted. If you only want a few
fields in the output file, the command line may be shortended by
preceding the appropriate qualifier with -only. For example, instead of
specifying -nohead -nousa -noname -noalign -nogaps -nogapcount
-nosimcount -noidcount -nodiffcount -noweight to get only the sequence
length output, you can specify -only -seqlength.
By default, the output file starts each line with the USA of the
sequence being described, so the output file is a list file that can be
manually edited and read in by any other EMBOSS program that can read
in one or more sequence to be analysed.
References
None.
Warnings
None.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
Program name Description
abiview Display the trace in an ABI sequencer file
coderet Extract CDS, mRNA and translations from feature tables
edialign Local multiple alignment of sequences
emma Multiple sequence alignment (ClustalW wrapper)
entret Retrieve sequence entries from flatfile databases and files
extractalign Extract regions from a sequence alignment
infoseq Display basic information about sequences
plotcon Plot conservation of a sequence alignment
prettyplot Draw a sequence alignment with pretty formatting
refseqget Get reference sequence
seqxref Retrieve all database cross-references for a sequence entry
seqxrefget Retrieve all cross-referenced data for a sequence entry
showalign Display a multiple sequence alignment in pretty format
tranalign Generate an alignment of nucleic coding regions from aligned
proteins
variationget Get sequence variations
whichdb Search all sequence databases for an entry and retrieve it
Author(s)
Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Please report all bugs to the EMBOSS bug team
(emboss-bug (c) emboss.open-bio.org) not to the original author.
History
Written (June 2001) - Gary Williams
Target users
This program is intended to be used by everyone and everything, from
naive users to embedded scripts.
Comments
None
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