Synopsis
Description
HHalign aligns a query alignment/HMM to a template alignment/HMM by HMM-HMM alignment. If only one alignment/HMM is given, it is compared to itself and the best off-diagonal alignment plus all further non-overlapping alignments above significance threshold are shown.Required Parameters
Input/query: single sequence or multiple sequence alignment (MSA) in a3m, a2m, or FASTA format, or HMM in hhm format
Input/template: single sequence or multiple sequence alignment (MSA) in a3m, a2m, or FASTA format, or HMM in hhm format
Input Alignment Format
Input alignment format:
a2mora3m: upper case = Match; lower case = Insert; ’-’ = Delete; ’.’ = gaps aligned to insertsfirst: FASTA format where columns with residue in 1st sequence are match states[0-100]: FASTA format where columns with fewer than X% gaps are match states
Neutralize His-, C-myc-, FLAG-tags, and trypsin recognition sequence to background distribution
Do NOT neutralize tags (default)
Output Options
Write results in standard format to file (default: <infile.hhr>)
Write query alignment in a3m format to file
Write query alignment in PSI-BLAST format to file
Append query alignment in a3m format to file
Append query alignment in PSI-BLAST format to file
Write pairwise alignments in FASTA format
Write pairwise alignments in A2M format
Write pairwise alignments in A3M format
Generate consensus sequence as master sequence of query MSA
Don’t show consensus sequence in alignments
Don’t show predicted 2ndary structure in alignments
Don’t show DSSP 2ndary structure in alignments
Show confidences for predicted 2ndary structure in alignments
Max. number of query/template sequences displayed
Number of columns per line in alignment list
Minimum probability in summary and alignment list (range: 0-100)
Maximum E-value in summary and alignment list (range: 0-inf)
Maximum number of lines in summary hit list
Minimum number of lines in summary hit list
Maximum number of alignments in alignment list
Minimum number of alignments in alignment list
Filter Options
Filter options applied to query MSA, template MSA, and result MSA.Show all sequences in result MSA; do not filter result MSA
Maximum pairwise sequence identity (range: 0-100)
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.
Minimum coverage with master sequence (%) (range: 0-100)
Minimum sequence identity with master sequence (%) (range: 0-100)
Minimum score per column with master sequence
Do not filter out sequences marked by ”>@” in their name line
HMM-HMM Alignment Options
Do NOT realign displayed hits with MAC algorithm
Realign displayed hits with max. accuracy (MAC) algorithm (default)
Posterior prob threshold for MAC realignment controlling greediness at alignment ends: 0=global, >0.1=local (range: 0-1)
Use global alignment mode for searching/ranking
Use local alignment mode for searching/ranking (default)
Exclude query positions from the alignment, e.g. ‘1-33,97-168’
Exclude template positions from the alignment, e.g. ‘1-33,97-168’
Banded alignment: forbid this many largest diagonals |i-j| of DP matrix
Show up to this many alternative alignments with raw score > smin
Minimum raw score for alternative alignments
Profile-profile score offset (range: -1 to 1)
Weight of term for pair correlations (range: 0-1)
Amino acid score (tja: template HMM at column j):
0: log2 Sum(tja*qia/pa) (pa: aa background frequencies)1: log2 Sum(tjaqia/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
Secondary structure scoring:
0: no ss scoring1,2: ss scoring after or during alignment3,4: ss scoring after or during alignment, predicted vs. predicted
Weight of ss score (range: 0-1)
SS confusion matrix = (1-ssa)I + ssapsipred-confusion-matrix (range: 0-1)
Use global sequence weighting for realignment
Gap Cost Options
Transition pseudocount admixture (range: 0-inf)
Transition pseudocount admixture for open gap (range: 0-inf)
Transition pseudocount admixture for extend gap (range: 0-1.5)
Factor to increase/reduce gap open penalty for deletes (range: >0)
Factor to increase/reduce gap open penalty for inserts (range: >0)
Factor to increase/reduce gap extend penalty for deletes (range: >0)
Factor to increase/reduce gap extend penalty for inserts (range: >0)
Penalty (bits) for end gaps aligned to query residues (range: 0-inf)
Penalty (bits) for end gaps aligned to template residues (range: 0-inf)
Pseudocount Options
Context-specific HHM pseudocounts
Position dependence of pc admixture ‘tau’ (pc mode):
0: no pseudo counts: tau = 01: constant: tau = a2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c)3: CSBlast admixture: tau = a(1+b)/(Neff[i]+b)
Overall pseudocount admixture (range: 0-1)
Neff threshold value for mode 2 (range: 1-inf)
Extinction exponent c for mode 2 (range: 0-3)
Context-independent HHM pseudocounts
Position dependence of pc admixture ‘tau’ (used for templates; used for query if contxt file is not available)
Overall pseudocount admixture (range: 0-1)
Neff threshold value for mode 2 (range: 1-inf)
Extinction exponent c for mode 2 (range: 0-3)
Context-specific pseudocounts
Use substitution-matrix instead of context-specific pseudocounts
Context file for computing context-specific pseudocounts
Weight of central position in cs pseudocount mode (range: 0-inf)
Weight decay parameter for positions in cs pc mode (range: 0-1)
Other Options
Verbose mode:
0: no screen output1: only warnings2: verbose
Write all alignments in tabular layout to file
Max number of input rows
Max number of HMM columns
Limit memory for realignment (in GB, range: 1-inf)
Examples
Align two alignments
Self-alignment to find internal repeats
Exit Codes
0: Success1: File format error2: File access error3: Memory error4: Command line error5: Internal numeric error
See Also
- hhsearch - Search a database of HMMs
- hhblits - Iterative sequence search
- hhmake - Build an HMM from an alignment
- HHR Format - Results output format