HHBLITS(1)

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

✨ hhblits(1) — User Commands ✨

okay bestie, welcome to the hhblits manual page, and honestly? It's giving protein-search royalty. 👑

🌸 NAME 🌸

hhblits — fast homology detection method to iteratively search a HMM database

🦋 SYNOPSIS 🦋

hhblits -i query [options]

💅 DESCRIPTION 💅

HHblits 3.3.0: HMM-HMM-based lightning-fast iterative sequence search

HHblits is a sensitive, general-purpose, iterative sequence search tool that represents both query and database sequences by HMMs. You can search HHblits databases starting with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging the significant database HMMs/MSAs onto the query MSA.

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 (c) The HH-suite development team

  • -i <file> — input/query: single sequence or multiple sequence alignment (MSA) in a3m, a2m, or FASTA format, or HMM in hhm format

<file> may be 'stdin' or 'stdout' throughout.

✨ OPTIONS ✨

  • -d <name> — database name (e.g. uniprot20_29Feb2012) Multiple databases may be specified with -d <db1> -d <db2> ... stack 'em up, bestie 💅
  • -n [1,8] — number of iterations (default=2) lowkey how many glow-up passes you want
  • -e [0,1] — E-value cutoff for inclusion in result alignment (def=0.001) the stricter, the pickier ✨

🎀 Input alignment format: 🎀

  • -M a2m — use A2M/A3M (default): upper case = Match; lower case = Insert; ' -' = Delete; '.' = gaps aligned to inserts (may be omitted) iykyk 🧬
  • -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) tag drama? handled 💅

🌈 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
  • -opsi <file> — write result MSA of significant matches in PSI-BLAST format
  • -ohhm <file> — write HHM file for result MSA of significant matches
  • -oalis <name> — write MSAs in A3M format after each iteration
  • -blasttab <name> — write result in tabular BLAST format (compatible to -m 8 or -outfmt 6 output)
1      2      3           4         5        6      8    9      10   11
              12

'query target #match/tLen #mismatch #gapOpen qstart qend tstart
tend eval score'
  • -add_cons — generate consensus sequence as master sequence of query MSA (default=don't) main character energy 👑
  • -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 vibe check on the folds 🌀
  • -Ofas <file> — write pairwise alignments in FASTA xor A2M (-Oa2m) xor A3M (-Oa3m) format
  • -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)

🔥 Prefilter options 🔥

  • -noprefilt — disable all filter steps no cap, zero filtering, chaos mode 💀
  • -noaddfilter — disable all filter steps (except for fast prefiltering)
  • -maxfilt — max number of hits allowed to pass 2nd prefilter (default=20000)
  • -min_prefilter_hits — min number of hits to pass prefilter (default=100)
  • -prepre_smax_thresh — min score threshold of ungapped prefilter (default=10)
  • -pre_evalue_thresh — max E-value threshold of Smith-Waterman prefilter score (default=1000.0)
  • -pre_bitfactor — prefilter scores are in units of 1 bit / pre_bitfactor (default=4)
  • -pre_gap_open — gap open penalty in prefilter Smith-Waterman alignment (default=20)
  • -pre_gap_extend — gap extend penalty in prefilter Smith-Waterman alignment (default=4)
  • -pre_score_offset — offset on sequence profile scores in prefilter S-W alignment (default=50)

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

  • -all — show all sequences in result MSA; do not filter result MSA everyone's invited to the function 🎉
  • -interim_filter NONE|FULL — filter sequences of query MSA during merging to avoid early stop (default: FULL)
    • NONE: disables the intermediate filter
    • FULL: if an early stop occurs compare filter seqs in an all vs. all comparison
  • -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=1000) diversity win 🦋
  • -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

👑 HMM-HMM alignment options: 👑

  • -norealign — do NOT realign displayed hits with MAC algorithm (def=realign)
  • -realign_old_hits — realign hits from previous iterations
  • -mact [0,1[ — posterior prob threshold for MAC realignment controlling greediness at alignment ends: 0:global >0.1:local (default=0.35) greedy at the ends? we been knew 💅
  • -glob/-loc — use global/local alignment mode for searching/ranking (def=local)
  • -realign — realign displayed hits with max. accuracy (MAC) algorithm
  • -realign_max <int> — realign max. <int> hits (default=500)
  • -ovlp <int> — banded alignment: forbid <ovlp> largest diagonals |i-j| of DP matrix (def=0)
  • -alt <int> — show up to this many alternative alignments with raw score > smin(def=4)
  • -premerge <int> — merge <int> hits to query MSA before aligning remaining hits (def=3)
  • -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)
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} — 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 confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=1.00)
  • -wg — use global sequence weighting for realignment! periodt.

💀 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)
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 prefilter pseudocounts: ✨

  • -pc_prefilter_contxt_mode {0,..,3} — position dependence of pc admixture 'tau' (pc mode, default=3)
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_prefilter_contxt_a [0,1] — overall pseudocount admixture (def=0.8)
  • -pc_prefilter_contxt_b [1,inf[ — Neff threshold value for mode 2 (def=2.0)
  • -pc_prefilter_contxt_c [0,3] — extinction exponent c for mode 2 (def=1.0)

✨ Context independent prefilter pseudocounts (used if context file is not available) ✨

okay so bestie, if there's no context file to feed it, these are the pseudocount knobs the prefilter falls back on. it's giving plan B but make it science 🧚

  • -pc_prefilter_nocontxt_mode {0,..,3} — how position-dependent the pc admixture tau is (pc mode, default=2). pick your fighter:
    1. 0: no pseudo counts, so tau = 0
    2. 1: constant, so tau = a
    3. 2: diversity-dependent, so tau = a/(1+((Neff[i]-1)/b)^c), where Neff[i] is the number of effective seqs in the local MSA around column i
  • -pc_prefilter_nocontxt_a — [0,1], the overall pseudocount admixture (def=1.0) 💖
  • -pc_prefilter_nocontxt_b — [1,inf[, the Neff threshold value for mode 2 (def=1.5)
  • -pc_prefilter_nocontxt_c — [0,3], the extinction exponent c for mode 2 (def=1.0)

✨ Context-specific pseudo-counts ✨

these are the ✨fancy✨ ones, where the neighbours of a column actually get a say:

  • -nocontxt — use substitution-matrix instead of context-specific pseudocounts
  • -contxt <file> — context file for computing context-specific pseudocounts (default= nothing, it's just empty)
  • -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 ✨

the lil grab-bag section, we love her 🌈

  • -v <int> — verbose mode: 0: no screen output, 1: only warings, 2: verbose (def=2). (yes the page literally says "warings" and we are keeping it exactly, no notes 💀)
  • -neffmax ]1,20] — skip further search iterations when the diversity Neff of the query MSA becomes larger than neffmax (default=20.0)
  • -cpu <int> — number of CPUs to use (for shared memory SMPs) (default=2) 🔥
  • -scores <file> — write scores for all pairwise comparisons to file
  • -filter_matrices — filter matrices for similarity, to output at most 100 matrices
  • -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)

✨ EXAMPLES ✨

here's the whole vibe in two lines, copy-paste and go 🫶

hhblits -i query.fas -o query.hhr -d ./uniclust30
hhblits -i query.fas -o query.hhr -oa3m query.a3m -n 1 -d ./uniclust30

and when you need the databases themselves, download them from:

http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/

and that's the whole page bestie, you ate 💅 this was hhblits version 3.3.0+ds, dated August 2023 — go forth and align, you absolute icon 👑✨

📦 where this page comes from