AB Consensus

--consensus, -con

Description

Condense alignments down to a single majority-rule consensus sequence (takes the most common residue in each column), or to a weighted consensus sequence (in which residues that belong to more divergent sequences are given more weight). If two or more residues are tied at a given column (equal frequencies or equal cumulative weights for this column), then an ambiguous 'X' (protein) or 'N' (nucleotide) is used at that position.

Arguments

Mode (mode_str)

The consensus function contains two modes: 'simple' and 'weighted'. The default mode is 'weighted'.

simple: Majority-rule consensus.

weighted: Weighted consensus. Residues that belong to more divergent sequences are given more weight, as described in Henikoff & Henikoff, J. Mol. Biol., 1994.

Example(s)

Input file: Panx_C-terms.stklm

# STOCKHOLM 1.0
#=GF SQ 3
Mle-Panxα9  ---atgttaga------catactttcaaagtttaaaggagttactccttttaaaggtataacgatag
Mle-Panxα7A atgggggtggaaattctgtttcccataatcaacagagccaccgctccgatcaagtctgttaacatcg
Mle-Panxα4  atggttattga------gctgctagctggatacaaaggtctgtccccgtttaaagacgcgactgttg
//
# STOCKHOLM 1.0
#=GF SQ 3
Mle-Panxα9  -mldilskf--kgvtpfkgitiddgwdqlnrsfmfvllvvmgttvtvr-qytgsviscdgfkkfg--stfaedycwtqg
Mle-Panxα7A mgveilfpiinratapiksvniddlssqlnrtfmfylsltfaititirqqlggayiacdgfsrdeeyerfaeewcwssg
Mle-Panxα4  mviellagy--kglspfkdatvddswdqinrcyvfiamvvmgavttmr-qysgtliacdgftkfh--pqfaedycwsig
//

Usage example

$: alignbuddy Panx_C-terms.stklm -con simple

Output

# STOCKHOLM 1.0
#=GF SQ 1
consensus atggtgNtNga------gNtNctNNcaaNNtacaaaggNNtNNctccgtttaaagNtgtNacNatNg
#=GS consensus AC consensus
#=GS consensus DE Original sequences: Mle-Panxα9, Mle-Panxα7A, Mle-Panxα4
//
# STOCKHOLM 1.0
#=GF SQ 1
consensus mXXeilXXX--kgXXpfkXXtiddXwdqlnrXfmfXlXvvmgXtXtXr-qyXgXXiacdgfXkfX--XXfaedycwsXg
#=GS consensus AC consensus
#=GS consensus DE Original sequences: Mle-Panxα9, Mle-Panxα7A, Mle-Panxα4
//