HHSEARCH(1)

📦
version 3.3.0 · 5 versions
, in ubuntu noble, ubuntu questing

💖 NAME 💖

hhsearch — she's a User Command and she's that girl: she searches a database of HMMs with a query alignment or query HMM. no cap. 🫶

🎀 SYNOPSIS 🎀

hhsearch -i query -d database [options]

✨ DESCRIPTION ✨

okay so bestie, here's the whole thing: HHsearch 3.3.0 — search a database of HMMs with a query alignment or query HMM. 💅

Copyright is held by 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. iconic. 📚

🌸 OPTIONS 🌸

  • -i <file> — your input / query multiple sequence alignment (that's a2m, a3m, or FASTA) or an HMM. this is the main character, the query, the one we're hunting with. 👑
fr fr, <file> may be 'stdin' or 'stdout' throughout. Options:
  • -d <name> — database name, like uniprot20_29Feb2012. and yes you can stack them, multiple databases may be specified with '-d <db1> -d <db2> ...' — go off, collect them all. 🌈
  • -e — [0,1] E-value cutoff for inclusion in result alignment (def=0.001). she's strict and that's a good thing.

🦋 Input alignment format 🦋

  • -M a2m — use A2M/A3M (this is the 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.
  • -tags / -notags — do NOT / do neutralize His-, C-myc-, FLAG-tags, and trypsin recognition sequence to background distribution (def=-notags). the tags are not the moment.

🍓 Output options 🍓

  • -o <file> — write results in standard format to file (default=<infile.hhr>).
  • -oa3m <file> — write result MSA with significant matches in a3m format.
  • -blasttab <name> — write result in tabular BLAST format (compatible to -m 8 or -outfmt 6 output). the columns are numbered 1 through 12:
1  2  3  4  5  6  7  8  9  10  11  12

and they mean:

query target #match/tLen alnLen #mismatch #gapOpen qstart qend tstart tend eval score
  • -opsi <file> — write result MSA of significant matches in PSI-BLAST format.
  • -ohhm <file> — write HHM file for result MSA of significant matches.
  • -add_cons — generate consensus sequence as master sequence of query MSA (default=don't).
  • -hide_cons — don't show consensus sequence in alignments (default=show).
  • -hide_pred — don't show predicted 2ndary structure in alignments (default=show).
  • -hide_dssp — don't show DSSP 2ndary structure in alignments (default=show).
  • -show_ssconf — show confidences for predicted 2ndary structure in alignments.
  • -Ofas <file> — write pairwise alignments in FASTA xor A2M (-Oa2m) xor A3M (-Oa3m) format. pick your fighter, not all three.
  • -seq <int> — max. number of query/template sequences displayed (default=1).
  • -aliw <int> — number of columns per line in alignment list (default=80).
  • -p [0,100] — minimum probability in summary and alignment list (default=20).
  • -E [0,inf[ — maximum E-value in summary and alignment list (default=1E+06).
  • -Z <int> — maximum number of lines in summary hit list (default=500).
  • -z <int> — minimum number of lines in summary hit list (default=10).
  • -B <int> — maximum number of alignments in alignment list (default=500).
  • -b <int> — minimum number of alignments in alignment list (default=10).

💜 Filter options applied to query MSA, database MSAs, and result MSA 💜

  • -all — show all sequences in result MSA; do not filter result MSA.
  • -id — [0,100] maximum pairwise sequence identity (def=90).
  • -diff [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)
  • -cov — [0,100] minimum coverage with master sequence (%) (def=0).
  • -qid — [0,100] minimum sequence identity with master sequence (%) (def=0).
  • -qsc — [0,100] minimum score per column with master sequence (default=-20.0).
  • -neff [1,inf] — target diversity of multiple sequence alignment (default=off).
  • -mark — do not filter out sequences marked by ">@" in their name line. protect them at all costs. 🛡️

🔥 HMM-HMM alignment options 🔥

  • -norealign — do NOT realign displayed hits with MAC algorithm (def=realign).
  • -ovlp <int> — banded alignment: forbid <ovlp> largest diagonals |i-j| of DP matrix (def=0).
  • -mact [0,1[ — posterior prob threshold for MAC realignment controlling greediness at alignment ends: 0:global >0.1:local (default=0.35).
  • -glob / -loc — use global/local alignment mode for searching/ranking (def=local).
  • -realign — realign displayed hits with max. accuracy (MAC) algorithm.
  • -excl <range> — exclude query positions from the alignment, e.g. '1-33,97-168'.
  • -realign_max <int> — realign max. <int> hits (default=500).
  • -alt <int> — show up to this many alternative alignments with raw score > smin (def=4).
  • -smin <float> — minimum raw score for alternative alignments (def=20.0).
  • -shift [-1,1] — profile-profile score offset (def=-0.03).
  • -corr [0,1] — weight of term for pair correlations (def=0.10).
  • -sc <int> — amino acid score (tja: template HMM at column j) (def=1). and the menu is:
    • 0 = log2 Sum(tja*qia/pa) (pa: aa background frequencies)
    • 1 = log2 Sum(tja*qia/pqa) (pqa = 1/2*(pa+ta) )
    • 2 = log2 Sum(tja*qia/ta) (ta: av. aa freqs in template)
    • 3 = log2 Sum(tja*qia/qa) (qa: av. aa freqs in query)
    • 5 = local amino acid composition correction
  • -ssm {0,..,4} — secondary structure scoring mode:
    • 0: no ss scoring
    • 1,2: ss scoring after or during alignment [default=2]
    • 3,4: ss scoring after or during alignment, predicted vs. predicted
  • -ssw [0,1] — weight of ss score (def=0.11).
  • -ssa [0,1] — SS substitution matrix = (1-ssa)*I + ssa*full-SS-substition-matrix [def=1.00)
  • -wg — use global sequence weighting for realignment! yes queen, weight it. ⚖️

🌈 Gap cost options 🌈

  • -gapb [0,inf[ — Transition pseudocount admixture (def=1.00).
  • -gapd [0,inf[ — Transition pseudocount admixture for open gap (default=0.15).
  • -gape [0,1.5] — Transition pseudocount admixture for extend gap (def=1.00).
  • -gapf ]0,inf] — factor to increase/reduce gap open penalty for deletes (def=0.60).
  • -gapg ]0,inf] — factor to increase/reduce gap open penalty for inserts (def=0.60).
  • -gaph ]0,inf] — factor to increase/reduce gap extend penalty for deletes (def=0.60).
  • -gapi ]0,inf] — factor to increase/reduce gap extend penalty for inserts (def=0.60).
  • -egq — [0,inf[ penalty (bits) for end gaps aligned to query residues (def=0.00).
  • -egt — [0,inf[ penalty (bits) for end gaps aligned to template residues (def=0.00).

🧚 Pseudocount (pc) options 🧚

Context specific hhm pseudocounts:

  • -pc_hhm_contxt_mode {0,..,3} — position dependence of pc admixture 'tau' (pc mode, default=2). the modes:
    • 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). the modes again:
    • 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=). yeah, the default is literally empty, that's not a typo bestie.
  • -csw — [0,inf] weight of central position in cs pseudocount mode (def=1.6).
  • -csb — [0,1] weight decay parameter for positions in cs pc mode (def=0.9).

⭐ Other options ⭐

  • -v <int> — verbose mode: 0:no screen output 1:only warnings 2: verbose (def=2).
  • -cpu <int> — number of CPUs to use (for shared memory SMPs) (default=2).
  • -scores <file> — write scores for all pairwise comparisons to file.
  • -atab <file> — write all alignments in tabular layout to file.
  • -maxseq <int> — max number of input rows (def=65535).
  • -maxres <int> — max number of HMM columns (def=20001).
  • -maxmem [1,inf[ — limit memory for realignment (in GB) (def=3.0).

🌟 Example 🌟

hhsearch -i a.1.1.1.a3m -d scop70_1.71

Download databases from <http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/>. go get your databases bestie, they're not gonna download themselves 🫶

and that's the whole page!! this one's hhsearch 3.3.0+ds, dated August 2023, and it lives in the HHSEARCH(1) chapter of the manual. tysm for reading, ily, now go find some remote homologs 💖✨🎀

📦 where this page comes from