Control File

Control files are structured as NEXUS-style blocks delineated by BEGIN and ENDBLOCK tokens.

Below is an annotated example of a DIGS control file for a polypeptide-based screen:

BEGIN SCREENDB;
    db_name=[your screening database name];
    mysql_server=[localhost];
ENDBLOCK;

BEGIN SCREENSETS;
    query_aa_fasta=[path to file with amino acid probes];
    reference_aa_fasta=[path to file with amino acid references];
    output_path=[path to output folder];
    bit_score_min_tblastn=100;
    seq_length_minimum=100;
    defragment_range=100;
ENDBLOCK;

BEGIN TARGETS;
    Mammals/Mus_musculus/complete/goldenpath_mm10/
    Mammals/Rattus_norvegicus/complete/goldenpath_rn6/
ENDBLOCK;

SCREENDB Block

The SCREENDB block defines the database connection details:

• db_name: The name of the screening database.
• mysql_server: The MySQL server (e.g., 'localhost' for local databases).

Ensure the MySQL user has the necessary privileges: CREATE, DROP, SELECT, ALTER, and DELETE.

SCREENSETS Block

The SCREENSETS block sets paths and parameters for BLAST-based screening:

• Paths to probe and reference libraries.
• Thresholds for BLAST significance.

BLAST takes a nucleotide or polypeptide sequence as query input and efficiently searches target databases for similar sequences. Results are reported in the form of a ranked list of ‘hits’, each associated with a statistical significance.

TARGETS Block

The TARGETS block specifies the paths to target files within a directory hierarchy. The DIGS tool will include every FASTA file under the specified path. For example:

BEGIN TARGETS;
    Mammals/
ENDBLOCK;

This includes all genomes stored under the path $DIGS_GENOMES/Mammals.

To target specific files, specify the complete paths:

BEGIN TARGETS;
    Mammals/Homo_sapiens/Complete/ncbi_37.3_june_11/ChrX.fa
    Mammals/Homo_sapiens/Complete/ncbi_37.3_june_11/ChrY.fa
ENDBLOCK;

Parameters Defined in the DIGS Control File

The DIGS control file contains parameters and paths for DIGS. Not all parameters are necessary for every screening configuration.

Parameter	Definition
SCREENDB BLOCK
db_name	Name of the screening database for this screening run
mysql_server:	MySQL server to use (e.g. 'localhost' for a local database)
SCREENSETS BLOCK
query_aa_fasta*	Path to FASTA file with amino acid probe sequences
query_na_fasta*	Path to FASTA file with nucleic acid probe sequences
reference_aa_fasta **	Path to FASTA file with amino acid reference sequences
reference_na_fasta **	Path to FASTA file with nucleic acid reference sequences
bit_score_min_tblastn*	Minimum bit score for recording hits (tBLASTn)
bit_score_min_blastn**	Minimum bit score for recording hits (BLASTn)
seq_length_minimum	Minimum length (nucleotides) for recording hits
defragment_range	Range within which two BLAST hits in the target sequence will be merged

Footnote: * Only required for screens utilizing protein sequences. ** Only required for screens utilizing nucleotide sequences.