cblaster¶
Welcome to cblaster’s documentation!
cblaster is a tool for identifying co-located hits in BLAST searches against NCBI sequence databases. It leverages the NCBI’s public APIs to facilitate fully remote searches, requiring no setup of local search databases.
If you find cblaster
helpful, please cite:
Cameron L.M. Gilchrist, Thomas J. Booth, Bram van Wersch, Liana van Grieken, Marnix H. Medema, Yit-Heng Chooi (2020).
cblaster: a remote search tool for rapid identification and visualisation of homologous gene clusters.
bioRxiv 2020.11.08.370601; doi: https://doi.org/10.1101/2020.11.08.370601
To view an example of what cblaster can produce, click here.
Features¶
- Fully remote searches against public NCBI sequence databases
- One command to generate local search databases from many genomes
- Easy to use graphical user interface (GUI)
- Fully interactive visualisations
User guide¶
- User Guide
- Table of Contents
- What is
cblaster
- Installation and Quick Start
- Pre-search configuration using the
config
module - Running a
cblaster
search using thesearch
module - Creating local sequence databases with the
makedb
module - Estimating genomic neighbourhood with the
gne
module - Retrieving hit sequences with the
extract
module - Extracting GenBank files from session files using
extract_clusters
- Plotting extracted clusters using
plot_clusters
- Using the graphical user interface (GUI)
- Miscellaneous functions
- What is
- Table of Contents
API Documentation¶
Comprehensive documentation for all public API exposed by cblaster:
- API Documentation
- cblaster.classes module
- cblaster.context module
- cblaster.database module
- cblaster.extract module
- cblaster.extract_clusters module
- cblaster.formatters module
- cblaster.genome_parsers module
- cblaster.helpers module
- cblaster.hmm_search module
- cblaster.intermediate_genes module
- cblaster.local module
- cblaster.main module
- cblaster.parsers module
- cblaster.plot module
- cblaster.plot_clusters module
- cblaster.remote module
- cblaster.sql module