discovering-enzymes

name	discovering-enzymes
description	Search and select enzyme sequence homologs from a database. Use when users provide a query sequence and want to discover sequence homologs of the query sequence in a database.

Discover enzyme homologs

Enzyme discovery toolkit to search, align, filter, and select enzyme sequence homologs in a database.

Input Format

• The input file (query.fasta) should have at least one query sequence in FASTA format.
• The database (targetDB) should be in the MMseqs2 database format. A database can be downloaded by running mmseqs databases <name> <o:sequenceDB> <tmpDir>. For example: `mmseqs databases UniProtKB databases/UniProtKB tmp

Workflow

Step 1: Search database

Searches a local database for sequence homologs of the query in the input file and saves the homologs in FASTA format. Requires MMSeqs2 (mmseqs).

python skills/discovering-enzymes/scripts/search_database.py query.fasta \
--db UniProtKB \
--targetDB databases/UniProtKB \
--iterations 1 \
--outdir homologs/ \

Step 2: Select homologs

Generates sequence alignments, filters the alignment and selects a number of sequence homologs. Saves the selected homologs in FASTA format. Requires MMSeqs2 (mmseqs) and HHfilter (hhfilter)

python skills/discovering-enzymes/scripts/select_homologs.py query.fasta homologs.fasta \
--hhfilter software/hhfilter \
--cov 50 \
--n 48 \
--outdir homologs/ \

Parameters

Search database

• db: Name of a database - UniProtKB, NR, or swissprot (default: UniProtKB)
• targetDB: Path to the database in the MMseqs2 database format (default: databases/UniProtKB)
• iterations: Number of iterations for a search (default: 1)
• outdir: Output directory (default: homologs/)

Select homologs

• hhfilter: Path to the HHfilter executable (default: software/hhfilter)
• cov: 'Minimum coverage with the query sequence (default: 50)
• n: 'Number of sequence homologs to be selected (default: 48)
• outdir: Output directory (default: homologs/)

Output Files

homologs/
├── homologs.fasta                       # All homologs from a search
└── homologs_DB_filtered_selected.fasta  # N selected homologs after filtering

Dependencies

biopython

Requirements

• MMseqs2 (mmseqs): Many-against-Many sequence searching and alignment
• HHfilter (hhfilter): Filter an alignment by maximum sequence identity and minimum coverage