INFOALIGN : Information on a multiple sequence alignment (EMBOSS)

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(

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= conditionally required)

input Section

advanced Section

output Section

input Section

sequence -- gapany [set of sequences] (-sequence) : please enter either :

the name of a file:
or the actual data here:

(sequence format)

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The number or the name of the reference sequence (-refseq)

Similarity scoring Matrix file (-matrix)
Plurality check % for consensus (-plurality)
Required % of identities at a position fro consensus (-identity)

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output Section

Output sequence details to a file (-outfile)
Format output as an HTML table (-html)
Display the specified columns (-only)
Display column headings (-heading)
Display the USA of the sequence (-usa)
Display 'name' column (-name)
Display 'seqlength' column (-seqlength)
Display 'alignlength' column (-alignlength)
Display number of gaps (-gaps)
Display number of gap positions (-gapcount)
Display number of identical positions (-idcount)
Display number of similar positions (-simcount)
Display number of different positions (-diffcount)
Display % number of changed positions (-change)
Display 'description' column (-description)

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Some explanations about the options

input Section
sequence -- gapany [set of sequences] (-sequence): The sequence alignment to be displayed.
enter either the name of a file or the actual data: if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button); OR you can type your data in the next area, or cut and paste it from another application.; (but not both)
advanced Section
The number or the name of the reference sequence (-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.
Plurality check % for consensus (-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.
Required % of identities at a position fro consensus (-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.
output Section
Output sequence details to a file (-outfile): If you enter the name of a file here then this program will write the sequence details into that file.
Display the specified columns (-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'
Sequence format: The sequence will be automatically converted in the format needed for the program; providing you enter a sequence either:; in plain (raw) sequence format or in one of the following known formats:; IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW; You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:54)