PASV Command Line Interface
The pasv
program has multiple commands to help you validate active sites, conserved residues, etc. in multiple sequence alignments.
Commands
The four pasv
commands are:
check
: Use pre-computed alignmentshmm
: Use hidden markov model (HMM) alignmentsmsa
: Use multiple sequence alignments (MSA)select
: Select sequences by their signatures
check
Use pasv check
when you already have an alignment file in which you want to check key residues or a region of interest (ROI).
Required arguments
pasv check
has two required arguments.
- A multiple sequence alignment in fasta format.
- The first sequence will be treated as the key reference sequence.
- All positions will be with respect to this sequence.
- key residues positions: a comma-separated list of key positions to check
For full CLI usage info, run pasv check --help
.
hmm
Use pasv hmm
when you want to use HMM alignments. In this mode, PASV uses the hmmalign
program of HMMER to compute sequence alignments.
The key reference sequence and all queries are aligned together against the reference HMM.
Required arguments
pasv hmm
has four required arguments:
- queries: the query sequences
- references: the reference HMM. This should be the output of HMMER's
hmmbuild
program - key reference sequence: a fasta file with the key reference sequence
- key residues positions: a comma-separated list of key positions to check
For full CLI usage info, run pasv hmm --help
.
Reference HMM
The references should be an HMM as output by hmmbuild
(or at least a program that generates compatible HMMs that can be used with HMMER and hmmalign
).
The HMMER user guide has detailed instructions on building HMMs, but the basic incantation for doing it is something like this:
$ hmmbuild [-options] <hmmfile_out> <msafile>
The HMM file output by this command is used as input to pasv-hmm
.
msa
Use pasv msa
when you want to align each query sequence individually with a set of reference sequences. In this mode, PASV uses one of Clustal Omega or MAFFT to align sequences.
Required arguments
pasv msa
has three required arguments:
- queries: the query sequences
- references
- The reference sequences to align with each query
- The first sequence in the fasta file should be the key reference sequence.
- key residues positions: a comma-separated list of key positions to check
For full CLI usage info, run pasv msa --help
.
select
Use pasv select
to select query sequences based on their key residue signatures.
After running one of the alignment subcommands (check
, hmm
, or msa
), you can run this command to select query sequences based on their signatures.
This is provided for parsing convenience. You can always parse the signatures file yourself with bash or your favorite scripting language.
Required arguments
pasv select
has three required arguments:
- queries: the query sequences
- signature file
- signatures: a comma-separated list of key positions to check
The signatures can be provided as fixed strings or regular expressions.
For full CLI usage info, run pasv select --help
.