hhmake - build an HMM from an input alignment or convert between
HMMER format and HHsearch format
HHmake 3.0.0 (15-03-2015) Build an HMM from an input alignment in
A2M, A3M, or FASTA format, or convert between HMMER format (.hmm) and
HHsearch format (.hhm). Remmert M, Biegert A, Hauser A, and Soding J.
HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM
alignment. Nat. Methods 9:173-175 (2011). (C) Johannes Soeding, Michael
Remmert, Andreas Biegert, Andreas Hauser
- -i <file>
- query alignment (A2M, A3M, or FASTA), or query HMM
- -o <file>
- HMM file to be written to (default=<infile.hhm>)
- -a <file>
- HMM file to be appended to
- -v <int>
- verbose mode: 0:no screen output 1:only warings 2: verbose
- -seq <int>
- max. number of query/template sequences displayed (def=10) Beware of
overflows! All these sequences are stored in memory.
- -add_cons
- make consensus sequence master sequence of query MSA
- -name
<name>
- use this name for HMM (default: use name of first sequence)
Filter query multiple sequence alignment
- -id
- [0,100] maximum pairwise sequence identity (%) (def=90)
- -diff [0,inf[
- filter MSA by selecting most diverse set of sequences, keeping at least
this many seqs in each MSA block of length 50 (def=100)
- -cov
- [0,100] minimum coverage with query (%) (def=0)
- -qid
- [0,100] minimum sequence identity with query (%) (def=0)
- -qsc
- [0,100] minimum score per column with query (def=-20.0)
- -neff [1,inf]
- target diversity of alignment (default=off)
- -M a2m
- use A2M/A3M (default): upper case = Match; lower case = Insert; '-' =
Delete; '.' = gaps aligned to inserts (may be omitted)
- -M first
- use FASTA: columns with residue in 1st sequence are match states
- -M [0,100]
- use FASTA: columns with fewer than X% gaps are match states
- Context specific hhm pseudocounts:
- -pc_hhm_contxt_mode
{0,..,3}
- position dependence of pc admixture 'tau' (pc mode, default=0)
- 0: no pseudo counts:
- tau = 0
- 1: constant
- tau = a
- 2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c) 3: CSBlast
admixture: tau = a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in
local MSA around column i)
- -pc_hhm_contxt_a
- [0,1] overall pseudocount admixture (def=0.9)
- -pc_hhm_contxt_b
- [1,inf[ Neff threshold value for mode 2 (def=4.0)
- -pc_hhm_contxt_c
- [0,3] extinction exponent c for mode 2 (def=1.0)
- Context independent hhm pseudocounts (used for templates; used for query
if contxt file is not available):
- -pc_hhm_nocontxt_mode
{0,..,3}
- position dependence of pc admixture 'tau' (pc mode, default=2)
- 0: no pseudo counts:
- tau = 0
- 1: constant
- tau = a
- 2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c) (Neff[i]: number of
effective seqs in local MSA around column i)
- -pc_hhm_nocontxt_a
- [0,1] overall pseudocount admixture (def=1.0)
- -pc_hhm_nocontxt_b
- [1,inf[ Neff threshold value for mode 2 (def=1.5)
- -pc_hhm_nocontxt_c
- [0,3] extinction exponent c for mode 2 (def=1.0)
- Context-specific pseudo-counts:
- -nocontxt
- use substitution-matrix instead of context-specific pseudocounts
-contxt <file> context file for computing
context-specific pseudocounts (default=./data/context_data.crf)
- -maxres
<int>
- max number of HMM columns (def=20001)
Example: hhmake -i test.a3m