A new version of the stand-alone BLAST applications is available. This release includes a number of improvements as well as a large number of bug fixes. See the BLAST+ user manual for details on the items below. The BLAST+ applications may be downloaded here. The improvements are:
1.) The custom tabular report now has support for query coverage, subject sequence title, and taxonomic information.
2.) Blastdbcmd has support for batch subsequence retrieval.
3.) The blastn application now uses a new "adaptive chunk size" for batch searches. This feature is important if the query file for the blastn application contains many FASTA entries. In that case, the BLAST application reads in many of the queries to search at once, and this improvement allows it to optimize the number of entries read at once. This features can speed up the search and reduce memory usage. See the BLAST+ user manual for details.
4.) Previous BLAST releases did not produce XML until the entire search was done. This behavior could cause the application to use too much memory if the query file contained many FASTA entries. BLAST+ 2.2.28 produces XML as soon as the search of each query is finished.
5.) RPSBLAST has software modifications to enable better composition-based statistics. Use of these statistics require changes to the conserved domain databases (CDD). Watch for an announcement from the NCBI.
A full list of BLAST+ 2.2.28 changes is at http://www.ncbi.nlm.nih.gov/books/NBK131777
1.) The custom tabular report now has support for query coverage, subject sequence title, and taxonomic information.
2.) Blastdbcmd has support for batch subsequence retrieval.
3.) The blastn application now uses a new "adaptive chunk size" for batch searches. This feature is important if the query file for the blastn application contains many FASTA entries. In that case, the BLAST application reads in many of the queries to search at once, and this improvement allows it to optimize the number of entries read at once. This features can speed up the search and reduce memory usage. See the BLAST+ user manual for details.
4.) Previous BLAST releases did not produce XML until the entire search was done. This behavior could cause the application to use too much memory if the query file contained many FASTA entries. BLAST+ 2.2.28 produces XML as soon as the search of each query is finished.
5.) RPSBLAST has software modifications to enable better composition-based statistics. Use of these statistics require changes to the conserved domain databases (CDD). Watch for an announcement from the NCBI.
A full list of BLAST+ 2.2.28 changes is at http://www.ncbi.nlm.nih.gov/books/NBK131777