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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.
% 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]: |
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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
Mandatory qualifiers: [-sequence] seqset The sequence alignment to be displayed. [-outfile] outfile If you enter the name of a file here then this program will write the sequence details into that file. Optional qualifiers: -refseq string If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. -matrix matrix This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. -html boolean Format output as an HTML table Advanced qualifiers: -plurality float Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. -identity float Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. -only boolean This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount' to get only the sequence length output, you can specify '-only -seqlength' -heading boolean Display column headings -usa boolean Display the USA of the sequence -name boolean Display 'name' column -seqlength boolean Display 'seqlength' column -alignlength boolean Display 'alignlength' column -gaps boolean Display number of gaps -gapcount boolean Display number of gap positions -idcount boolean Display number of identical positions -simcount boolean Display number of similar positions -diffcount boolean Display number of different positions -change boolean Display % number of changed positions -description boolean Display 'description' column General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
The sequence alignment to be displayed. | Readable sequences | Required |
[-outfile] (Parameter 2) |
If you enter the name of a file here then this program will write the sequence details into that file. | Output file | <sequence>.infoalign |
Optional qualifiers | Allowed values | Default | |
-refseq | If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. | Any string is accepted | 0 |
-matrix | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
-html | Format output as an HTML table | Boolean value Yes/No | No |
Advanced qualifiers | Allowed values | Default | |
-plurality | Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. | Number from 0.000 to 100.000 | 50.0 |
-identity | Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. | Number from 0.000 to 100.000 | 0.0 |
-only | This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount' to get only the sequence length output, you can specify '-only -seqlength' | Boolean value Yes/No | No |
-heading | Display column headings | Boolean value Yes/No | @(!$(only)) |
-usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) |
-name | Display 'name' column | Boolean value Yes/No | @(!$(only)) |
-seqlength | Display 'seqlength' column | Boolean value Yes/No | @(!$(only)) |
-alignlength | Display 'alignlength' column | Boolean value Yes/No | @(!$(only)) |
-gaps | Display number of gaps | Boolean value Yes/No | @(!$(only)) |
-gapcount | Display number of gap positions | Boolean value Yes/No | @(!$(only)) |
-idcount | Display number of identical positions | Boolean value Yes/No | @(!$(only)) |
-simcount | Display number of similar positions | Boolean value Yes/No | @(!$(only)) |
-diffcount | Display number of different positions | Boolean value Yes/No | @(!$(only)) |
-change | Display % number of changed positions | Boolean value Yes/No | @(!$(only)) |
-description | Display 'description' column | Boolean value Yes/No | @(!$(only)) |
!!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~~~ |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 150 154 3 4 48 10 92 68.000000 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 150 154 3 4 48 10 92 68.000000 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 144 147 2 3 45 7 92 68.750000 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 144 147 2 3 48 4 92 66.666664 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 157 161 3 4 25 13 119 84.076431 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 151 153 1 2 21 13 117 86.092712 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 11 20 122 92.810455 |
# Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description HBB_HUMAN 150 154 3 4 48 10 92 68.000000 HBB_HORSE 150 154 3 4 48 10 92 68.000000 HBA_HUMAN 144 147 2 3 45 7 92 68.750000 HBA_HORSE 144 147 2 3 48 4 92 66.666664 MYG_PHYCA 157 161 3 4 25 13 119 84.076431 GLB5_PETMA 151 153 1 2 21 13 117 86.092712 LGB2_LUPLU 153 153 0 0 11 20 122 92.810455 |
HBB_HUMAN 150 HBB_HORSE 150 HBA_HUMAN 144 HBA_HORSE 144 MYG_PHYCA 157 GLB5_PETMA 151 LGB2_LUPLU 153 |
HBB_HUMAN 4 92 HBB_HORSE 4 92 HBA_HUMAN 3 92 HBA_HORSE 3 92 MYG_PHYCA 4 119 GLB5_PETMA 2 117 LGB2_LUPLU 0 122 |
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>150</td> <td>154</td> <td>3</td> <td>4</td> <td>48</td> <td>10</td> <td>92</td> <td>68.000000</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:HBB_HORSE</td> <td>HBB_HORSE</td> <td>150</td> <td>154</td> <td>3</td> <td>4</td> <td>48</td> <td>10</td> <td>92</td> <td>68.000000</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:HBA_HUMAN</td> <td>HBA_HUMAN</td> <td>144</td> <td>147</td> <td>2</td> <td>3</td> <td>45</td> <td>7</td> <td>92</td> <td>68.750000</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:HBA_HORSE</td> <td>HBA_HORSE</td> <td>144</td> <td>147</td> <td>2</td> <td>3</td> <td>48</td> <td>4</td> <td>92</td> <td>66.666664</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:MYG_PHYCA</td> <td>MYG_PHYCA</td> <td>157</td> <td>161</td> <td>3</td> <td>4</td> <td>25</td> <td>13</td> <td>119</td> <td>84.076431</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:GLB5_PETMA</td> <td>GLB5_PETMA</td> <td>151</td> <td>153</td> <td>1</td> <td>2</td> <td>21</td> <td>13</td> <td>117</td> <td>86.092712</td> <td></td> </tr> <tr><td>msf::../../data/globins.msf:LGB2_LUPLU</td> <td>LGB2_LUPLU</td> <td>153</td> <td>153</td> <td>0</td> <td>0</td> <td>11</td> <td>20</td> <td>122</td> <td>92.810455</td> <td></td> </tr> </table> |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 150 154 3 4 150 0 0 0.000000 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 150 154 3 4 126 10 14 16.000000 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 144 147 2 3 51 19 74 64.583336 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 144 147 2 3 54 18 72 62.500000 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 157 161 3 4 34 22 101 78.343948 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 151 153 1 2 26 27 98 82.781456 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 21 28 104 86.274513 |
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 |