CONS : Creates a consensus from multiple alignments (EMBOSS)
Some explanations about the options
input Section- msf -- gapany [set of sequences] (-msf)
- File containing a sequence alignment.
- 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- Plurality check value (-plurality)
- Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment.
- Required number of identities at a position (-identity)
- Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.
output Section- Define a threshold above which the consensus is given in uppercase (-setcase)
- Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case.
- 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.- msf -- gapany [set of sequences] (-msf)
Pise form generator version: 5.a (16 Dec 2002 11:53)
