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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 globin.seq
Don't display the USA of a sequence
% infoalign globin.seq -nousa -out stdout
Display only the name and sequence length of a sequence
% infoalign globin.seq -only -name -seqlength -out stdout
Display only the name, number of gap characters and differences to the consensus sequence
% infoalign globin.seq -only -name -gapcount -diffcount -out stdout
Display the name and number of gaps within a sequence
% infoalign globin.seq -only -name -gaps -out stdout
Display information formatted with HTML
% infoalign globin.seq -html -out stdout
Use the first sequence as the reference sequence to compare to
% infoalign globin.seq -refseq 1 -out stdout
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 | 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' | Yes/No | No |
-heading | Display column headings | Yes/No | @(!$(only)) |
-usa | Display the USA of the sequence | Yes/No | @(!$(only)) |
-name | Display 'name' column | Yes/No | @(!$(only)) |
-seqlength | Display 'seqlength' column | Yes/No | @(!$(only)) |
-alignlength | Display 'alignlength' column | Yes/No | @(!$(only)) |
-gaps | Display number of gaps | Yes/No | @(!$(only)) |
-gapcount | Display number of gap positions | Yes/No | @(!$(only)) |
-idcount | Display number of identical positions | Yes/No | @(!$(only)) |
-simcount | Display number of similar positions | Yes/No | @(!$(only)) |
-diffcount | Display number of different positions | Yes/No | @(!$(only)) |
-change | Display % number of changed positions | Yes/No | @(!$(only)) |
-description | Display 'description' column | Yes/No | @(!$(only)) |
# USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Description fasta::globin.seq:HBB_MACFU HBB_MACFU 147 148 1 1 134 3 10 8.843537 fasta::globin.seq:HBD_HUMAN HBD_HUMAN 147 148 1 1 128 7 12 12.925170 fasta::globin.seq:HBB_RABIT HBB_RABIT 147 148 1 1 131 7 9 10.884354 fasta::globin.seq:HBB_BOVIN HBB_BOVIN 146 147 1 1 121 10 15 17.123287 fasta::globin.seq:HBB_LAMGL HBB_LAMGL 151 152 1 1 122 11 18 19.205297 fasta::globin.seq:HBE_HUMAN HBE_HUMAN 143 150 2 7 104 14 25 27.272728 fasta::globin.seq:HBE_RABIT HBE_RABIT 147 148 1 1 113 16 18 23.129251
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 |