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HHCONSENSUS

NAME

hhconsensus − calculate the consensus sequence for an A3M/FASTA input file

SYNOPSIS

hhconsensus −i <file> [options]

DESCRIPTION

HHconsensus 3.0.0 (15−03−2015) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser 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).
−i
<file>

query alignment (A2M, A3M, or FASTA), or query HMM

Output options:
−s
<file>

append consensus sequence in FASTA (default=<infile.seq>)

−o <file>

write alignment with consensus sequence in A3M

−oa3m <file>

same

−oa2m <file>

write alignment with consensus sequence in A2M

−ofas <file>

write alignment with consensus sequence in FASTA

−v <int>

verbose mode: 0:no screen output 1:only warings 2: verbose

Filter input alignment (options can be combined):

−id

[0,100] maximum pairwise sequence identity (%) (def=100)

−diff

[0,inf[ filter most diverse set of sequences, keeping at least this

many sequences in each block of >50 columns (def=0)

−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)

Input alignment format:

−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

Other options:

−maxres <int> max number of HMM columns (def=20001)

Example: hhconsensus −i stdin −s stdout

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