.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.2. .TH HHSEARCH "1" "March 2021" "hhsearch 3.3.0+ds" "User Commands" .SH NAME hhsearch \- search a database of HMMs with a query alignment or query HMM .SH SYNOPSIS .B hhsearch \fI\,\-i query \-d database \/\fR[\fI\,options\/\fR] .SH DESCRIPTION HHsearch 3.3.0 Search a database of HMMs with a query alignment or query HMM (c) The HH\-suite development team Steinegger M, Meier M, Mirdita M, V??hringer H, Haunsberger S J, and S??ding J (2019) HH\-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics, doi:10.1186/s12859\-019\-3019\-7 .TP \fB\-i\fR input/query multiple sequence alignment (a2m, a3m, FASTA) or HMM .PP may be 'stdin' or 'stdout' throughout. Options: .TP \fB\-d\fR database name (e.g. uniprot20_29Feb2012) Multiple databases may be specified with '\-d \fB\-d\fR ...' .TP \fB\-e\fR [0,1] E\-value cutoff for inclusion in result alignment (def=0.001) .SS "Input alignment format:" .TP \fB\-M\fR a2m use A2M/A3M (default): upper case = Match; lower case = Insert; .IP \&'\-' = Delete; '.' = gaps aligned to inserts (may be omitted) .TP \fB\-M\fR first use FASTA: columns with residue in 1st sequence are match states .TP \fB\-M\fR [0,100] use FASTA: columns with fewer than X% gaps are match states .TP \fB\-tags\fR/\-notags do NOT / do neutralize His\-, C\-myc\-, FLAG\-tags, and trypsin recognition sequence to background distribution (def=\-notags) .SS "Output options:" .TP \fB\-o\fR write results in standard format to file (default=) .TP \fB\-oa3m\fR write result MSA with significant matches in a3m format .HP \fB\-blasttab\fR write result in tabular BLAST format (compatible to \fB\-m\fR 8 or \fB\-outfmt\fR 6 output) .TP 1 2 3 4 5 6 7 8 9 10 11 12 .IP query target #match/tLen alnLen #mismatch #gapOpen qstart qend tstart tend eval score .TP \fB\-opsi\fR write result MSA of significant matches in PSI\-BLAST format .TP \fB\-ohhm\fR write HHM file for result MSA of significant matches .TP \fB\-add_cons\fR generate consensus sequence as master sequence of query MSA (default=don't) .TP \fB\-hide_cons\fR don't show consensus sequence in alignments (default=show) .TP \fB\-hide_pred\fR don't show predicted 2ndary structure in alignments (default=show) .TP \fB\-hide_dssp\fR don't show DSSP 2ndary structure in alignments (default=show) .TP \fB\-show_ssconf\fR show confidences for predicted 2ndary structure in alignments .TP \fB\-Ofas\fR write pairwise alignments in FASTA xor A2M (\fB\-Oa2m\fR) xor A3M (\fB\-Oa3m\fR) format .TP \fB\-seq\fR max. number of query/template sequences displayed (default=1) .TP \fB\-aliw\fR number of columns per line in alignment list (default=80) .TP \fB\-p\fR [0,100] minimum probability in summary and alignment list (default=20) .TP \fB\-E\fR [0,inf[ maximum E\-value in summary and alignment list (default=1E+06) .TP \fB\-Z\fR maximum number of lines in summary hit list (default=500) .TP \fB\-z\fR minimum number of lines in summary hit list (default=10) .TP \fB\-B\fR maximum number of alignments in alignment list (default=500) .TP \fB\-b\fR minimum number of alignments in alignment list (default=10) .PP Filter options applied to query MSA, database MSAs, and result MSA .TP \fB\-all\fR show all sequences in result MSA; do not filter result MSA .TP \fB\-id\fR [0,100] maximum pairwise sequence identity (def=90) .TP \fB\-diff\fR [0,inf[ filter MSAs by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50 Zero and non\-numerical values turn off the filtering. (def=100) .TP \fB\-cov\fR [0,100] minimum coverage with master sequence (%) (def=0) .TP \fB\-qid\fR [0,100] minimum sequence identity with master sequence (%) (def=0) .TP \fB\-qsc\fR [0,100] minimum score per column with master sequence (default=\-20.0) .TP \fB\-neff\fR [1,inf] target diversity of multiple sequence alignment (default=off) .TP \fB\-mark\fR do not filter out sequences marked by ">@"in their name line .SS "HMM\-HMM alignment options:" .TP \fB\-norealign\fR do NOT realign displayed hits with MAC algorithm (def=realign) .TP \fB\-ovlp\fR banded alignment: forbid largest diagonals |i\-j| of DP matrix (def=0) .TP \fB\-mact\fR [0,1[ posterior prob threshold for MAC realignment controlling greediness at alignment ends: 0:global >0.1:local (default=0.35) .TP \fB\-glob\fR/\-loc use global/local alignment mode for searching/ranking (def=local) .TP \fB\-realign\fR realign displayed hits with max. accuracy (MAC) algorithm .TP \fB\-excl\fR exclude query positions from the alignment, e.g. '1\-33,97\-168' .TP \fB\-realign_max\fR realign max. hits (default=500) .TP \fB\-alt\fR show up to this many alternative alignments with raw score > smin(def=4) .TP \fB\-smin\fR minimum raw score for alternative alignments (def=20.0) .TP \fB\-shift\fR [\-1,1] profile\-profile score offset (def=\-0.03) .TP \fB\-corr\fR [0,1] weight of term for pair correlations (def=0.10) .TP \fB\-sc\fR amino acid score (tja: template HMM at column j) (def=1) .TP 0 = log2 Sum(tja*qia/pa) (pa: aa background frequencies) .TP 1 = log2 Sum(tja*qia/pqa) (pqa = 1/2*(pa+ta) ) .TP 2 = log2 Sum(tja*qia/ta) (ta: av. aa freqs in template) .TP 3 = log2 Sum(tja*qia/qa) (qa: av. aa freqs in query) .TP 5 local amino acid composition correction .TP \fB\-ssm\fR {0,..,4} 0: no ss scoring .TP 1,2: ss scoring after or during alignment [default=2] .IP 3,4: ss scoring after or during alignment, predicted vs. predicted .TP \fB\-ssw\fR [0,1] weight of ss score (def=0.11) .TP \fB\-ssa\fR [0,1] SS substitution matrix = (1\-ssa)*I + ssa*full\-SS\-substition\-matrix [def=1.00) .TP \fB\-wg\fR use global sequence weighting for realignment! .SS "Gap cost options:" .TP \fB\-gapb\fR [0,inf[ Transition pseudocount admixture (def=1.00) .TP \fB\-gapd\fR [0,inf[ Transition pseudocount admixture for open gap (default=0.15) .TP \fB\-gape\fR [0,1.5] Transition pseudocount admixture for extend gap (def=1.00) .TP \fB\-gapf\fR ]0,inf] factor to increase/reduce gap open penalty for deletes (def=0.60) .TP \fB\-gapg\fR ]0,inf] factor to increase/reduce gap open penalty for inserts (def=0.60) .TP \fB\-gaph\fR ]0,inf] factor to increase/reduce gap extend penalty for deletes(def=0.60) .TP \fB\-gapi\fR ]0,inf] factor to increase/reduce gap extend penalty for inserts(def=0.60) .TP \fB\-egq\fR [0,inf[ penalty (bits) for end gaps aligned to query residues (def=0.00) .TP \fB\-egt\fR [0,inf[ penalty (bits) for end gaps aligned to template residues (def=0.00) .SS "Pseudocount (pc) options:" .IP Context specific hhm pseudocounts: .TP \fB\-pc_hhm_contxt_mode\fR {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2) .TP 0: no pseudo counts: tau = 0 .TP 1: constant tau = a .IP 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) .TP \fB\-pc_hhm_contxt_a\fR [0,1] overall pseudocount admixture (def=0.9) .TP \fB\-pc_hhm_contxt_b\fR [1,inf[ Neff threshold value for mode 2 (def=4.0) .TP \fB\-pc_hhm_contxt_c\fR [0,3] extinction exponent c for mode 2 (def=1.0) .IP Context independent hhm pseudocounts (used for templates; used for query if contxt file is not available): .TP \fB\-pc_hhm_nocontxt_mode\fR {0,..,3} position dependence of pc admixture 'tau' (pc mode, default=2) .TP 0: no pseudo counts: tau = 0 .TP 1: constant tau = a .IP 2: diversity\-dependent: tau = a/(1+((Neff[i]\-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i) .TP \fB\-pc_hhm_nocontxt_a\fR [0,1] overall pseudocount admixture (def=1.0) .TP \fB\-pc_hhm_nocontxt_b\fR [1,inf[ Neff threshold value for mode 2 (def=1.5) .TP \fB\-pc_hhm_nocontxt_c\fR [0,3] extinction exponent c for mode 2 (def=1.0) .IP Context\-specific pseudo\-counts: .TP \fB\-nocontxt\fR use substitution\-matrix instead of context\-specific pseudocounts .HP \fB\-contxt\fR context file for computing context\-specific pseudocounts (default=) .TP \fB\-csw\fR [0,inf] weight of central position in cs pseudocount mode (def=1.6) .TP \fB\-csb\fR [0,1] weight decay parameter for positions in cs pc mode (def=0.9) .SS "Other options:" .TP \fB\-v\fR verbose mode: 0:no screen output 1:only warnings 2: verbose (def=2) .TP \fB\-cpu\fR number of CPUs to use (for shared memory SMPs) (default=2) .HP \fB\-scores\fR write scores for all pairwise comparisons to file .TP \fB\-atab\fR write all alignments in tabular layout to file .TP \fB\-maxseq\fR max number of input rows (def=65535) .TP \fB\-maxres\fR max number of HMM columns (def=20001) .HP \fB\-maxmem\fR [1,inf[ limit memory for realignment (in GB) (def=3.0) .PP Example: hhsearch \fB\-i\fR a.1.1.1.a3m \fB\-d\fR scop70_1.71 .PP Download databases from .