|
|
infoalign |
It will write a table containing one line per sequence. The information is written out in columns separated by space or TAB characters. The columns of data are: the sequences' USA, name, two measures of length, counts of gaps, and numbers of identical, similar and different residues or bases in this sequence when compared to a reference sequence, together with a simple statistic of the % change between the reference sequence and this sequence.
The reference sequence can be either the calculated consensus sequence (the default) or it can be one of the set of aligned sequences, specified by either the ordinal number of that sequence in the input file, or by its name.
Any combination of these types of information can be easily selected or unselected.
By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by any other EMBOSS program that can read in one or more sequence to be analysed.
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 ../../data/globins.msf Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the input files for this example
Go to the output files for this example
Example 2
This example doesn't display the USA of the sequence:
% infoalign ../../data/globins.msf -nousa Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 3
Display only the name and sequence length of a sequence:
% infoalign ../../data/globins.msf -only -name -seqlength Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 4
Display only the name, number of gap characters and differences to the consensus sequence:
% infoalign ../../data/globins.msf -only -name -gapcount -diffcount Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 5
Display the name and number of gaps within a sequence:
% infoalign ../../data/globins.msf -only -name -gaps Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 6
Display information formatted with HTML:
% infoalign ../../data/globins.msf -html Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 7
Use the first sequence as the reference sequence to compare to:
% infoalign ../../data/globins.msf -refseq 1 Information on a multiple sequence alignment Output file [globins.infoalign]: |
Go to the output files for this example
Example 8
% infoalign -auto tembl:eclac* -out test.out |
Go to the input files for this example
Go to the output files for this example
Example 9
% infoalign -auto tembl:eclacz -out test.out |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-sequence] seqset The sequence alignment to be displayed.
[-outfile] outfile If you enter the name of a file here then
this program will write the sequence details
into that file.
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.
-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.
-html boolean Format output as an HTML table
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.
-identity float Provides the facility of setting the
required number of identities at a position
for it to give a consensus. Therefore, if
this is set to 100% only columns of
identities contribute to the consensus.
-only boolean This is a way of shortening the command line
if you only want a few things to be
displayed. Instead of specifying:
'-nohead -nousa -noname -noalign -nogaps
-nogapcount -nosimcount -noidcount
-nodiffcount'
to get only the sequence length output, you
can specify
'-only -seqlength'
-heading boolean Display column headings
-usa boolean Display the USA of the sequence
-name boolean Display 'name' column
-seqlength boolean Display 'seqlength' column
-alignlength boolean Display 'alignlength' column
-gaps boolean Display number of gaps
-gapcount boolean Display number of gap positions
-idcount boolean Display number of identical positions
-simcount boolean Display number of similar positions
-diffcount boolean Display number of different positions
-change boolean Display % number of changed positions
-description boolean Display 'description' column
Associated qualifiers:
"-sequence" 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
-sformat1 string Input sequence format
-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 standard output
-filter boolean Read standard input, write 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. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
The sequence alignment to be displayed. | Readable set of sequences | Required |
| [-outfile] (Parameter 2) |
If you enter the name of a file here then this program will write the sequence details into that file. | Output file | <sequence>.infoalign |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -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 | If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. | Any string is accepted | 0 |
| -html | Format output as an HTML table | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -plurality | Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. | Number from 0.000 to 100.000 | 50.0 |
| -identity | Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. | Number from 0.000 to 100.000 | 0.0 |
| -only | This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount' to get only the sequence length output, you can specify '-only -seqlength' | Boolean value Yes/No | No |
| -heading | Display column headings | Boolean value Yes/No | @(!$(only)) |
| -usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) |
| -name | Display 'name' column | Boolean value Yes/No | @(!$(only)) |
| -seqlength | Display 'seqlength' column | Boolean value Yes/No | @(!$(only)) |
| -alignlength | Display 'alignlength' column | Boolean value Yes/No | @(!$(only)) |
| -gaps | Display number of gaps | Boolean value Yes/No | @(!$(only)) |
| -gapcount | Display number of gap positions | Boolean value Yes/No | @(!$(only)) |
| -idcount | Display number of identical positions | Boolean value Yes/No | @(!$(only)) |
| -simcount | Display number of similar positions | Boolean value Yes/No | @(!$(only)) |
| -diffcount | Display number of different positions | Boolean value Yes/No | @(!$(only)) |
| -change | Display % number of changed positions | Boolean value Yes/No | @(!$(only)) |
| -description | Display 'description' column | Boolean value Yes/No | @(!$(only)) |
!!AA_MULTIPLE_ALIGNMENT 1.0
../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 ..
Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.14
Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.15
Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.15
Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.19
Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 0.23
Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.21
Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.10
//
1 50
HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD
51 100
HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN
101 150
HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA
151 164
HBB_HUMAN NALAHKYH~~~~~~
HBB_HORSE NALAHKYH~~~~~~
HBA_HUMAN TVLTSKYR~~~~~~
HBA_HORSE TVLTSKYR~~~~~~
MYG_PHYCA KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~
|
ID ECLACZ standard; DNA; PRO; 3078 BP.
XX
AC V00296;
XX
SV V00296.1
XX
DT 13-JUL-1983 (Rel. 03, Created)
DT 06-MAR-1996 (Rel. 47, Last updated, Version 4)
XX
DE E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW galactosidase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC Escherichia.
XX
RN [1]
RP 1-3078
RX MEDLINE; 84028567.
RA Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT "Sequence of the lacZ gene of Escherichia coli";
RL EMBO J. 2:593-597(1983).
XX
RN [2]
RX MEDLINE; 87275876.
RA Zell R., Fritz H.J.;
RT "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT deamination of 5-methyl-cytosine residues";
RL EMBO J. 6:1809-1815(1987).
XX
DR SWISS-PROT; P00722; BGAL_ECOLI.
XX
CC Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH Key Location/Qualifiers
FH
FT source 1..3078
FT /db_xref="taxon:562"
FT /organism="Escherichia coli"
FT CDS <1..3072
FT /db_xref="SWISS-PROT:P00722"
FT /note="galactosidase"
FT /transl_table=11
FT /protein_id="CAA23573.1"
FT /translation="TMITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTD
FT RPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVT
FT YPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQ
FT DSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQI
FT SDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDE
[Part of this file has been deleted for brevity]
gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt 180
gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag 240
gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac 300
accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg 360
ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga 420
attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt 480
tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga 540
gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag 600
gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca 660
caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg 720
gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta 780
tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat 840
gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg 900
tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc 960
acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt 1020
ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat 1080
cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag 1140
cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg 1200
ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg 1260
gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta 1320
acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat 1380
gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct 1440
tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc 1500
ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc 1560
aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac 1620
gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc 1680
cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa 1740
aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag 1800
ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca 1860
aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc 1920
gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt 1980
aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt 2040
gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta 2100
gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg 2160
cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg 2220
accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc 2280
cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg 2340
cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc 2400
attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca 2460
gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac 2520
gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt 2580
agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg 2640
cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta 2700
gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg 2760
ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg 2820
acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc 2880
cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa 2940
ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc 3000
ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg 3060
tgtcaaaaat aataataa 3078
//
|
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3 4 48 10 88 68.000000 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3 4 48 10 88 68.000000 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2 3 45 7 89 68.750000 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2 3 48 4 89 66.666664 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3 4 25 13 115 84.076431 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1 2 21 13 115 86.092712 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 11 20 122 92.810455 |
# Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description HBB_HUMAN 146 150 3 4 48 10 88 68.000000 HBB_HORSE 146 150 3 4 48 10 88 68.000000 HBA_HUMAN 141 144 2 3 45 7 89 68.750000 HBA_HORSE 141 144 2 3 48 4 89 66.666664 MYG_PHYCA 153 157 3 4 25 13 115 84.076431 GLB5_PETMA 149 151 1 2 21 13 115 86.092712 LGB2_LUPLU 153 153 0 0 11 20 122 92.810455 |
HBB_HUMAN 146 HBB_HORSE 146 HBA_HUMAN 141 HBA_HORSE 141 MYG_PHYCA 153 GLB5_PETMA 149 LGB2_LUPLU 153 |
HBB_HUMAN 4 88 HBB_HORSE 4 88 HBA_HUMAN 3 89 HBA_HORSE 3 89 MYG_PHYCA 4 115 GLB5_PETMA 2 115 LGB2_LUPLU 0 122 |
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>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>48</td> <td>10</td> <td>88</td> <td>68.000000</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>48</td> <td>10</td> <td>88</td> <td>68.000000</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>45</td> <td>7</td> <td>89</td> <td>68.750000</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>48</td> <td>4</td> <td>89</td> <td>66.666664</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>25</td> <td>13</td> <td>115</td> <td>84.076431</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>21</td> <td>13</td> <td>115</td> <td>86.092712</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:LGB2_LUPLU</td> <td>LGB2_LUPLU</td> <td>153</td> <td>153</td> <td>0</td> <td>0</td> <td>11</td> <td>20</td> <td>122</td> <td>92.810455</td> <td></td> </tr> </table> |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3 4 146 0 0 2.666667 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3 4 122 10 14 18.666666 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2 3 48 19 74 66.666664 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2 3 51 18 72 64.583336 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3 4 30 22 101 80.891716 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1 2 24 27 98 84.105957 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 21 28 104 86.274513 |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description tembl-id:ECLAC ECLAC 7477 7477 0 0 65 0 7412 99.130669 E.coli lactose operon with lacI, lacZ, lacY and lacA genes. tembl-id:ECLACA ECLACA 1832 1832 0 0 71 0 1761 96.124451 Escherichia coli lacA gene for thiogalactoside transacetylase tembl-id:ECLACI ECLACI 1113 1113 0 0 67 0 1046 93.980232 E. coli laci gene (codes for the lac repressor). tembl-id:ECLACY ECLACY 1500 1500 0 0 68 0 1432 95.466667 E. coli lacY gene (codes for lactose permease). tembl-id:ECLACZ ECLACZ 3078 3078 0 0 72 0 3006 97.660820 E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23). |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description tembl-id:ECLACZ ECLACZ 3078 3078 0 0 0 0 3078 100.000000 E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23). |
The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters:
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:
| Program name | Description |
|---|---|
| emma | Multiple alignment program - interface to ClustalW program |
| infoseq | Displays some simple information about sequences |
| plotcon | Plots the quality of conservation of a sequence alignment |
| prettyplot | Displays aligned sequences, with colouring and boxing |
| seealso | Finds programs sharing group names |
| showalign | Displays a multiple sequence alignment |
| showdb | Displays information on the currently available databases |
| textsearch | Search sequence documentation text. SRS and Entrez are faster! |
| tfm | Displays a program's help documentation manual |
| tranalign | Align nucleic coding regions given the aligned proteins |
| whichdb | Search all databases for an entry |
| wossname | Finds programs by keywords in their one-line documentation |