msaf2 0.1.0

Building and managing MSA prior to stucture inference

Multiple Sequence Ali/Alpha Fold

Streamlining the MSA building stages

installation

External dependencies

MSAF uses the following tools:

• mmseqs2 for database search
• mafft for multiple sequence alignment You will need those two sotware installed

Python package

Just, pip install msaf

Global setup

MSAF requires a configuration file as first parameter. This configuration file is under yaml format of the following shape

databases : 
  - /path/to/databases/mmseqs
executables:
  mafft: /usr/local/bin/mafft
  mmseqs: /opt/homebrew/bin/mmseqs
settings:
  cache : /path/to/msaf/cache
cocktails:
    test:
        ingredients:
        - target: swissprot
            label: pif.sto
        - target: uniprot
            label: paf.a3m

Where,

• databases is a list of folder, where MSAF recursively looks for mmseqs database
• executables are key, value of paths to executable external dependencies
• cache points to a folder used to store MSAF mess, it MUST exist
• cocktails is dictionary of recipes

MSAF recipes

Recipes are declared in the configuration file. A recipe is caracterized by a name (eg:test) and ingredients. ingredients define database search and save schema as list of target and label. The target key defines the database to search and label defines the resulting msa file (and format). Recipes feature an optional PDQT parameter, which if set to TRUE will wrap all a3m files in an aligned.pdqt file

In the above exemple, the test recipe will trigger a search in swissprot and uniprot for all supplied queries.

• The result of swissprot search will be save under stockholm format in a file named pif.sto
• The result of the uniprot search will be save under a3m format in a file named paf.a3m

Usage

List available database

At startup, MSAF will recurively search inside all databases item found in configuration file for mmseqs database files (<database_name>_h, <database_name>_.index, <database_name>.lookup, <database_name>.index).

The registred <database_name> can be displayed with python -m msaf config.yaml --list

run a search

python -m msaf config.yaml --query query1.fasta query2.fasta --bp test With --bp refering to one recipe defined in the config file and --query to absolute path(s) of query sequence file(s) (fasta format).

Multimer search

Results will be saved in the --output folder (msas, by default) with subfolders using sequential one letter chain identifier along the sequence of query files. If the same file is provided more than once as a query, only one folder will be created. Hence, results of an homodimer search will be stored under a single A/ subfolder.