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https://github.com/gamcil/cblasterA tool for finding clusters of co-located homologous sequences in BLAST searches. It supports remote searches via NCBI APIs and local searches using DIAMOND, providing genomic context, synteny scoring for GenBank files, and interactive HTML visualizations of clustered hits.
cblaster is a tool designed to identify clusters of co-located sequences using BLAST searches. It is primarily used to find instances of genes encoding related proteins that are clustered on a specific scaffold, which is particularly useful for discovering natural product biosynthetic gene clusters in bacteria and fungi.
Core capabilities include:
cblaster provides several command-line modules to perform different stages of the clustering workflow:
cblaster search: Queries a FASTA file of protein sequences against either the NCBI database or a local database to identify co-located sequences. It produces various graphical and textual outputs.cblaster makedb: Used to rapidly create local databases from GenBank files to facilitate future searches.cblaster gne: Analyzes how varying intergenic distances affects search output. This helps evaluate the robustness of results and understand the distribution of gene cluster sizes.cblaster extract: Produces FASTA files containing the protein sequences of identified homologues for use in downstream applications.The cblaster search process follows a specific pipeline depending on whether you are running in remote or local mode:
cblaster scans scaffolds for clustered hits and generates summary tables and visualizations.makedb module) is used to group hits by organism, scaffold, and subject sequences.cblaster scans scaffolds for clustered hits and generates summary tables and visualizations.WARNING Before running any search, you must run the
cblaster configmodule to provide either an e-mail address or an NCBI API key.
It is important to distinguish between search/filtering thresholds and clustering thresholds:
Arguments like -me/--max_evalue, -mi/--min_identity, and -mc/--min_coverage determine which individual BLAST hits are kept. Any hit not meeting these criteria is discarded immediately.
Arguments like -g/--gap, -u/--unique, and -mh/--min_hits determine if a group of hits qualifies as a 'cluster'.
-g/--gap: The maximum distance (in base pairs) allowed between any two hits in a cluster. This should be tuned based on your organism (e.g., lower for bacteria/fungi, higher for plants).-u/--unique: The minimum number of different query sequences that must be represented in a cluster. If you have 5 queries and set -u 3, a cluster must contain hits from at least 3 distinct queries to be kept.-mh/--min_hits: The minimum total number of hits in a cluster, regardless of which query they came from.-r/--require: A list of specific query sequences that must be present in a cluster for that cluster to be retained.Example: Requiring specific sequences in a cluster:
cblaster search -qf query.fasta -r Seq1 Seq3 Seq5(Only clusters containing Seq1, Seq3, AND Seq5 will be kept.)
By default, cblaster performs remote searches via the NCBI BLAST API. If you wish to perform local searches, you must have diamond installed and available in your system $PATH.
cblaster will throw an error if a local search is initiated but cannot find diamond or diamond-aligner (the alias used when installed via apt).
cblaster provides the following capabilities:
To check the currently installed version of cblaster, use the --version flag.
$ cblaster --versionRemote searches are the default mode. Use the following options to customize them:
-d/--database to choose a protein database (e.g., nr, refseq_protein, swissprot, pdbaa). Note that cblaster only supports protein searches via BLASTp.--rid argument to resume.-eq/--entrez_query to filter the NCBI database using Entrez search terms (e.g., taxonomic IDs). This can significantly reduce run times.Example: Filtering for Fungi (Taxonomy ID 4751):
cblaster search -qf query.fasta -eq "txid4751[orgn]"# Resume a search using an RID
cblaster search -qf query.fasta --rid RAV3P2F3014
# Filter search to specific taxa using Entrez
cblaster search -qf query.fasta -eq "txid4751[orgn]"You can provide query sequences to the cblaster search command in two ways:
-qf/--query_file argument to point to a file containing amino acid sequences.-qi/--query_ids argument to provide NCBI identifiers (e.g., accession, GI number). These can be provided in a newline-separated text file or directly on the command line.Both methods launch a remote search against NCBI by default.
# Using a FASTA file
cblaster search -qf myFile.fasta
# Using a text file containing newline-separated IDs
cblaster search -qi myFile.txt
# Using IDs directly on the command line
cblaster search -qi query1 query2 ...Every module in the cblaster command line interface provides a help dialogue detailing available arguments. To access the help documentation for a specific command, provide -h or --help as the sole argument following that command.
$ cblaster -h
$ cblaster search -h
$ cblaster gne -h
$ cblaster makedb -h
$ cblaster extract -hThe makedb module generates the local databases required for cblaster searches from genome files. It accepts two types of arguments: the input genome files and a base name for the output files.
.gbk files directly..gff files. Note that for GFF3 files, cblaster requires matching .fasta files containing the nucleotide sequences for each region in the same working directory (e.g., if you provide one.gff, one.fasta must exist).When you specify a name (e.g., myDb), the module generates the following files:
myDb.sqlite3: Local database for looking up genomic context of hits.myDb.dmnd: DIAMOND sequence search database.myDb.fasta: All protein sequences parsed from genomes, used for HMMER searches.$ cblaster makedb one.gbk two.gbk three.gbk four.gbk myDb