A new version of the stand-alone applications is available.
BLAST+ applications may be downloaded here. Instructions on the installation of BLAST+ applications are available here.
The BLAST+ 2.2.26 release contains a number of important changes and improvements:
1.) DELTA-BLAST. A new application called deltablast is included in this release. Deltablast stands for Domain Enhanced Look-up Time Accelerated BLAST. It first uses RPS-BLAST to align a protein query to conserved domains in CDD, then performs a sequence database search using a position specific score matrix (PSSM) derived from the aligned domains. The PSSM construction method is similar to that of PSI-BLAST, but begins by aligning the query to CD's rather than to individual sequences. DELTA-BLAST can be much more sensitive than standard BLASTP. DELTA-BLAST is also available from the "protein blast" link at blast.ncbi.nlm.nih.gov. DELTA-BLAST needs a special version of CDD database that contains some extra files. Instructions for downloading and installing this specialized copy of the CDD database can be found in section 5.18 of the BLAST Command Line Application Manual at http://www.ncbi.nlm.nih.gov/books/NBK1763/
2.) New finite size correction (FSC). The FSC is subtracted from the query and database sequence length for the calculation of the BLAST statistics used to rank the results. The older FSC did not properly handle short query or database sequences, as the estimated FSC might be longer than a short sequence, and it was necessary to simply set the resulting length to an ad hoc value (typically one). The new approach elides this issue by looking at the expected values of both the query and database length together, rather than separately. In general, it ranks matches involving a short query or database sequence as more significant. The new FSC increases the ROC score (at 4853 FP) found with a SCOP test set by about 2%. For short queries or database sequences, it may change the expect value reported by orders of magnitude. Currently, the new FSC is only implemented for protein-protein programs (e.g., blastp, psiblast, blastx, rpsblast, etc.), but not the blastn application. The old behavior may be recovered by setting the environment variable OLD_FSC to a non NULL value.
3.) Makeprofiledb. Makeprofiledb can be used to make search sets for RPS-BLAST, including the specialized data needed by DELTA-BLAST. Makeprofiledb is a replacement for the C toolkit application formatrspdb.
4.) Blastcl3 users should switch to BLAST+. Blastcl3 is deprecated and the service will need to be retired in the not too distant future. This client and service have served the community well since 1997, but changes in the way BLAST searches are done at the NCBI (e.g., a Request ID can be issued for a search) mean that a better and more robust client can be offered. The BLAST+ applications can send off remote searches if the argument -remote is added. More details are available at http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
5.) Last C toolkit binary release. This is the last release of the C toolkit BLAST binaries (e.g., blastall, blastpgp, etc.). The source code for these application is not being updated anymore, but will continue to be available. Users of these legacy binaries are encouraged to move to the BLAST+ applications that are being actively developed. Help on transitioning to the BLAST+ applications can be found at http://www.ncbi.nlm.nih.gov/books/NBK1763/
ChangeLog:
-----------------------------
* 2.2.26 release.
* Mac executables are now Universal Binaries for 32- and 64-bit architectures, we no longer produce PPC and Intel Universal binaries. The executable archive names remain unchanged.
* Added DELTA-BLAST - a new tool for sensitive protein searches
* Added makeprofiledb - a tool for creating a database for RPS-BLAST
Improvements:
* The blast_formatter application can now format bl2seq RIDs.
* PSI-BLAST can produce archive format, blast_formatter can format that output.
* PSI-BLAST has two new options that work with multiple-sequence alignments: ignore_msa_master and msa_master_idx (see BLAST+ manual).
* mkmbindex can now create masked indices from a BLAST database and ASN.1 masking data.
* An improved finite size correction is now used for blastp/blastx/tblastn/rpsblast. The FSC is subtracted from the query and database sequence length for the calculation of the expect value. The new FSC results in more accurate expect values, especially for alignments with a short query or target sequence. Re-enable the old size correction by setting the environment variable OLD_FSC to a non-NULL value.
* The blastdbcmd -range parameter now accepts a blank value for the second parameter to signify the end of a sequence (e.g., -range "100-")
* There was a performance improvement for long database sequences in results with many matches.
Bug fixes:
* There was a blastn problem if subject_loc and lcase_masking were used together.
* There was a problem with multi-threaded blastx if the query included a long (10,000+) sequence of N's.
* The percent identity calculation was wrong if the best-hit algorithm was used.
* There was a problem with the multiple BLAST database statistics report in XML format.
* Makeblastdb failed to return an error when input was not available.
* The formatting option -outfmt "7 nident" always printed zero.
* The search strategy was not properly saving the -db_soft_mask option.
* An error message was emitted if there was a "<" in the query title.
* A problem reading lower-case masking from the query could cause a search to fail.
BLAST+ applications may be downloaded here. Instructions on the installation of BLAST+ applications are available here.
The BLAST+ 2.2.26 release contains a number of important changes and improvements:
1.) DELTA-BLAST. A new application called deltablast is included in this release. Deltablast stands for Domain Enhanced Look-up Time Accelerated BLAST. It first uses RPS-BLAST to align a protein query to conserved domains in CDD, then performs a sequence database search using a position specific score matrix (PSSM) derived from the aligned domains. The PSSM construction method is similar to that of PSI-BLAST, but begins by aligning the query to CD's rather than to individual sequences. DELTA-BLAST can be much more sensitive than standard BLASTP. DELTA-BLAST is also available from the "protein blast" link at blast.ncbi.nlm.nih.gov. DELTA-BLAST needs a special version of CDD database that contains some extra files. Instructions for downloading and installing this specialized copy of the CDD database can be found in section 5.18 of the BLAST Command Line Application Manual at http://www.ncbi.nlm.nih.gov/books/NBK1763/
2.) New finite size correction (FSC). The FSC is subtracted from the query and database sequence length for the calculation of the BLAST statistics used to rank the results. The older FSC did not properly handle short query or database sequences, as the estimated FSC might be longer than a short sequence, and it was necessary to simply set the resulting length to an ad hoc value (typically one). The new approach elides this issue by looking at the expected values of both the query and database length together, rather than separately. In general, it ranks matches involving a short query or database sequence as more significant. The new FSC increases the ROC score (at 4853 FP) found with a SCOP test set by about 2%. For short queries or database sequences, it may change the expect value reported by orders of magnitude. Currently, the new FSC is only implemented for protein-protein programs (e.g., blastp, psiblast, blastx, rpsblast, etc.), but not the blastn application. The old behavior may be recovered by setting the environment variable OLD_FSC to a non NULL value.
3.) Makeprofiledb. Makeprofiledb can be used to make search sets for RPS-BLAST, including the specialized data needed by DELTA-BLAST. Makeprofiledb is a replacement for the C toolkit application formatrspdb.
4.) Blastcl3 users should switch to BLAST+. Blastcl3 is deprecated and the service will need to be retired in the not too distant future. This client and service have served the community well since 1997, but changes in the way BLAST searches are done at the NCBI (e.g., a Request ID can be issued for a search) mean that a better and more robust client can be offered. The BLAST+ applications can send off remote searches if the argument -remote is added. More details are available at http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastNews
5.) Last C toolkit binary release. This is the last release of the C toolkit BLAST binaries (e.g., blastall, blastpgp, etc.). The source code for these application is not being updated anymore, but will continue to be available. Users of these legacy binaries are encouraged to move to the BLAST+ applications that are being actively developed. Help on transitioning to the BLAST+ applications can be found at http://www.ncbi.nlm.nih.gov/books/NBK1763/
ChangeLog:
-----------------------------
* 2.2.26 release.
* Mac executables are now Universal Binaries for 32- and 64-bit architectures, we no longer produce PPC and Intel Universal binaries. The executable archive names remain unchanged.
* Added DELTA-BLAST - a new tool for sensitive protein searches
* Added makeprofiledb - a tool for creating a database for RPS-BLAST
Improvements:
* The blast_formatter application can now format bl2seq RIDs.
* PSI-BLAST can produce archive format, blast_formatter can format that output.
* PSI-BLAST has two new options that work with multiple-sequence alignments: ignore_msa_master and msa_master_idx (see BLAST+ manual).
* mkmbindex can now create masked indices from a BLAST database and ASN.1 masking data.
* An improved finite size correction is now used for blastp/blastx/tblastn/rpsblast. The FSC is subtracted from the query and database sequence length for the calculation of the expect value. The new FSC results in more accurate expect values, especially for alignments with a short query or target sequence. Re-enable the old size correction by setting the environment variable OLD_FSC to a non-NULL value.
* The blastdbcmd -range parameter now accepts a blank value for the second parameter to signify the end of a sequence (e.g., -range "100-")
* There was a performance improvement for long database sequences in results with many matches.
Bug fixes:
* There was a blastn problem if subject_loc and lcase_masking were used together.
* There was a problem with multi-threaded blastx if the query included a long (10,000+) sequence of N's.
* The percent identity calculation was wrong if the best-hit algorithm was used.
* There was a problem with the multiple BLAST database statistics report in XML format.
* Makeblastdb failed to return an error when input was not available.
* The formatting option -outfmt "7 nident" always printed zero.
* The search strategy was not properly saving the -db_soft_mask option.
* An error message was emitted if there was a "<" in the query title.
* A problem reading lower-case masking from the query could cause a search to fail.