BCMBase

Database Selection Guide

BMCBase offers three specialized gene databases; please choose the one that best suits your research environment:

🌿 Mangrove Gene Database (Mangrove Gene Database)

Suitable for research: Mangrove ecosystems, intertidal zones, and salt-tolerant plant rhizosphere microorganisms

Distinctive genes: Contains genes related to salt tolerance, antioxidant activity, and organic matter degradation unique to mangroves

Recommended use: Ideal for studies involving mangrove sediments, rhizosphere soils, and phyllosphere microbial communities

🌊 Saltmarsh Gene Database (Saltmarsh Gene Database)

Suitable for research: Salt marsh wetlands, high-salinity environments, and extremophile microorganisms

Distinctive genes: Rich in genes associated with extreme salt tolerance, osmotic regulation, and sulfur cycling

Recommended use: The top choice for researching salt lakes, salt marshes, and microorganisms in high-salinity seawater environments

🌱 Seagrass Gene Database (Seagrass Gene Database)

Suitable for research: Seagrass bed ecosystems, marine sediments, and marine plant microbiomes

Distinctive genes: Encompasses genes related to the seagrass rhizosphere, marine carbon and nitrogen cycles, and marine primary production

Recommended use: Recommended for studies of seagrass bed sediments and the rhizosphere of marine plants

Usage Instructions

Select Database: Use the "Select Comparison Database" dropdown menu to choose the database that best suits your research environment
Enter Sequence: Paste your sequence in the textbox or select a FASTA file using the "Upload File" option
Set Parameters: Choose the BLAST program (blastp for protein sequences, blastx for DNA sequences)
Adjust Thresholds: Modify the E-value threshold and maximum target sequence count as needed
Run Search: Click "Run BLAST" to start the alignment; it usually takes 1-2 minutes

Features

Users can upload sequence files (e.g., .fa, .fasta, .faa, .txt formats) or directly enter sequence data to perform BLAST-based searches on the gene catalogs in the database, with the option to use either BLASTX or BLASTP mode.

Supports multiple sequence input formats (FASTA, plain text)
Offers three specialized ecological gene databases
Automatically filters out low similarity results (<50% similarity)
Supports exporting results in TSV format
Displays search progress and parameter information in real-time

Tips

Select the appropriate database: Choose the database corresponding to your sample's environment to significantly improve matching accuracy
Sequence Length: It is recommended to use sequences longer than 50 amino acids or 150 nucleotides for the search
E-value Settings: For conserved sequences, use a stricter threshold (1e-10), and for novel sequences, relax it to 1e-3
Interpreting Results: Prioritize results with over 70% similarity, as these typically have higher functional relevance