The article "BLAST+: architecture and applications" by Christiam Camacho et al. discusses the redesign and improvements of the BLAST (Basic Local Alignment Search Tool) software. The authors address the limitations of the current BLAST command-line applications, particularly in handling long query sequences and database sequences, and introduce new features to enhance performance and user interface. Key improvements include: 1. **Query Splitting**: Long query sequences are broken into smaller chunks to reduce CPU time and memory usage. 2. **Partial Subject Sequence Retrieval**: Only relevant parts of long database sequences are retrieved, further reducing CPU time and memory usage. 3. **Masking Information**: The program can now retrieve masking information from BLAST databases. 4. **Modular Software Library**: A new modular software library allows access to subject sequence data from various sources. 5. **Strategy Files**: Users can save and reuse favorite sets of options, which can be uploaded to and downloaded from the NCBI BLAST web site. The new BLAST command-line applications demonstrate significant speed improvements for long queries and chromosome-length database sequences. The article also highlights the benefits of database masking and the flexibility of query splitting. Future developments include adding hard-masking support for databases and multi-threading the trace-back phase. The new BLAST+ software is available as Public Domain software and can be accessed from the NCBI FTP site.The article "BLAST+: architecture and applications" by Christiam Camacho et al. discusses the redesign and improvements of the BLAST (Basic Local Alignment Search Tool) software. The authors address the limitations of the current BLAST command-line applications, particularly in handling long query sequences and database sequences, and introduce new features to enhance performance and user interface. Key improvements include: 1. **Query Splitting**: Long query sequences are broken into smaller chunks to reduce CPU time and memory usage. 2. **Partial Subject Sequence Retrieval**: Only relevant parts of long database sequences are retrieved, further reducing CPU time and memory usage. 3. **Masking Information**: The program can now retrieve masking information from BLAST databases. 4. **Modular Software Library**: A new modular software library allows access to subject sequence data from various sources. 5. **Strategy Files**: Users can save and reuse favorite sets of options, which can be uploaded to and downloaded from the NCBI BLAST web site. The new BLAST command-line applications demonstrate significant speed improvements for long queries and chromosome-length database sequences. The article also highlights the benefits of database masking and the flexibility of query splitting. Future developments include adding hard-masking support for databases and multi-threading the trace-back phase. The new BLAST+ software is available as Public Domain software and can be accessed from the NCBI FTP site.