| {"file": "helpblast_NBK1762/Blast_ReleaseNotes.nxml", "text": "BLAST+ 2.14.1: August 21, 2023\nNew features\nAdded documentation for cleanup-blastdb-volumes.py script: https://www.ncbi.nlm.nih.gov/books/NBK592857/\nImprovements\nUse https for increased performance and reliability when downloading data from NCBI via update_blastdb.pl\nBug fixes\nFix bug in update_blastdb.pl when downloading data from NCBI\nFix blastn and blastx crashes when using -mt_mode option\nBLAST+ 2.14.0: April 25, 2023\nNew features\nBLASTP, BLASTX, and TBLASTN are now quicker when you use the \"fast\" tasks with a command-line argument like \"-task blastp-fast.\" You can search the non-redundant protein database(nr) over 20% faster than before. Smaller databases like swissprot or pdbaa will be 2-3 times faster.\nImprovements\nA FASTA file that cannot be validated by makeblastdb is now a warning and not an error.\nUpdate_blastdb.pl uses curl on a mac to download BLASTDB files instead of a PERL module.\nAn error is issued if the incompatible -remote and -in_pssm options are used together.\nA formatting pre-fetch error is no longer fatal, and BLAST will try to format the report.\nBug fixes\nFixed an issue with a space before the database name that crashed the rpsblast executable.\nFixed a multi-threading consistency issue with the -use_sw_tback option.\nFixed an issue that crashed the blastn executable.\nFixed an issue sorting results with composition-based statistics.\nFixed an exit code issue with update_blast.pl\nCorrected the expect value setting for blastn-short task\nFixed an issue with sstrand in tabular formats with the tblastn executable.\nBLAST+ 2.13.0: March 11, 2022\nNew features\nBlastn_vdb and tblastn_vdb included in the 2.13.0 release.\nMakeblastdb now produces a (JSON) metadata file about the database. This makes BLAST databases more Findable in the FAIR sense. See here for details.\nImprovements\nTBLASTN can now handle database sequences up to 2 billion bases (was 1 billion)\nMakeblastdb default volume size is now 3 billion bases (was 1 billion)\nDustmasker has a new option to replace low complexity regions with N's (hard masking)\nMakeblastdb will issue an error message and exit if it encounters a sequence longer than the maximum supported size (2,147,483,647 letters).\nBug fixes\nRare problem with mutex that caused BLAST to crash.\nMemory leaks.\nBLAST+ 2.12.0: June 28, 2021\nFor this release, we have performed a major restructuring of the module that reads the BLAST databases. For multithreaded searches, these changes reduce the number of mutex calls, result in the use of fewer file pointers, and reduce the number of calls to memory map. These changes also allow us to support a different threading model (\u201cthreading by query\u201d) that can be more efficient in some situations. See https://www.ncbi.nlm.nih.gov/books/NBK571452/ for more information.\nNOTE: The NCBI is preparing to use a larger numerical range for its GI identifier. This release provides full support for these GI's that will appear in nucleotide databases later this year.\nNew features\nThreading by query batch (for BLASTN, BLASTP, BLASTX, RPSBLAST, and RPSTBLASTN) may more efficiently BLAST large numbers of queries, especially if the database is small or the search is limited by taxid. Use \"-mt_mode 1\" to enable this option.\nMakeblastdb requires less virtual memory for smaller databases.\nMakeprofiledb creates multiple volumes for a CDD database, which allows RPSBLAST to handle a larger number of records. The number of SMP files included in a volume can be controlled with the new -new_smp_vol option.\nupdate_blastdb.pl now supports the \"-showall pretty\" option for databases hosted at the NCBI.\nupdate_blastdb.pl now reports the database timestamp in ISO8601 format.\nBug fixes\nFixed phiblast core dump when -subject option is used.\nFixed memory leak in setup procedures.\nBLAST+ 2.11.0: October 19, 2020\nNew features\nUsage reporting - Help improve BLAST by sharing limited information about your search. Details on the information collected, how it is used, and how to opt-out at https://www.ncbi.nlm.nih.gov/books/ NBK309243\nThreading by query batch for rpsblast/rpstblast can BLAST large numbers of queries faster. For large numbers of queries, use the -mt option to more efficiently multi-thread the search.\nBug fixes\nFix slowdown in TBLASTN searches run without composition-based statistics on long database sequences.\nRemove necessity of a network connection for blast_formatter. This also speeds up blast_formatter if the database can be found locally.\nA core dump for RPSBLAST and RPSTBLASTN has been fixed.\nMakeblastdb for windows has been fixed to not require as much virtual memory and to not produce overly large LMDB files.\nBLAST+ 2.10.1: June 8, 2020\nBug fixes\nFix for TBLASTN Multi-Threading bug.\nBLAST+ 2.10.0: December 16, 2019\nNew features\nEnhancements to composition-based statistics to ensure the consistency of matches if fewer than the default number of matches is selected. Read about the details in the \u201cOutline of the BLAST process\u201d section of the BLAST+ user manual appendix.\nAdaptive composition-based statistics may process more sequences in the CBS stage of BLAST if many matches have a similar score, increasing the likelihood of finding novel results. To enable: set the environment variable ADAPTIVE_CBS to 1. This is an experimental feature and your feedback is welcome.\nDefault BLAST database version changes:\nmakeblastdb generates BLAST databases in version 5 format.\nNew script to clean up BLAST database volumes (cleanup-blastdb-volumes.py).\nAdd support for genetic code 33 for blastx and rpstblastn.\nImprovements\nBetter error messages for -taxids argument.\nConsistent error reporting in get_species_taxids.sh to standard error.\nBug fixes\nRestore sum statistics (-sum_stat parameter) for BLASTN.\nFix Blast-archive generation/ingestion when subject_besthits flag is used.\nFix problem with empty lines in files provided to the taxidlist argument.\nFix blastdb_aliastool input file size overflow problem.\nFix blastdb_aliastool problem in Windows with binary GI list files.\nFix search failures using -remote option in BLAST+ 2.9.0.\nFix reading from standard input in Windows.\nFix missing space in descriptions defline.\nFix HTML BLAST report to include version in accession anchors.\nFix segmentation fault in tabular BLAST output format when sequences have no defline.\nFix to prevent generation of local Seq-IDs in Seq-align output format when accessions are available.\nFix blast_formatter output when searches are limited by taxonomy.\nBLAST+ 2.9.0: April 1, 2019\nNew features\nSupport for PDB biopolymer chain identifiers up to four-characters long in BLASTDB version 5 (not supported in BLASTDB version 4).\nConfigurable output separator for tabular and CSV output formats (see manual entry).\nImprovements\nBetter error messages in get_species_taxids.sh.\nFix memory leaks in BLAST libraries and unit tests.\nBug fixes\nFix taxID filtering combined with mask-based alias BLAST databases.\nFix ordering of sequence IDs in BLAST report.\nBLAST+ 2.8.1: December 13, 2018\nNOTE: First production release to support the new\u00a0BLAST\u00a0database version (BLASTDBv5). This is a taxonomically aware version of the BLAST database. See notes at\u00a0https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf\nImprovements\nA new option (-subject_besthit) culls HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another\u00a0HSP. This is an experimental option and is subject to change.\nAllow use of the -max_target_seqs option for formats 0-4. The number of alignments and descriptions will be set to the max_target_seqs.\nIssue a warning if -max_target_seqs is set to less than five.\nBug fixes\nDisabled an overly aggressive optimization that caused problems mentioned by Shah et al. in\u00a0https://www.ncbi.nlm.nih.gov/pubmed/30247621.\nFixed an invalid memory error that occurred when\u00a0composition-based statistics\u00a0and\u00a0SEG\u00a0were used.\nFixed some memory problems with the culling option.\nNucleotide scores for even rewards are no longer rounded down to an even number when displayed.\nBlastdbcmd now reports intervals in the output\u00a0FASTA\u00a0if a partial sequence is requested with the range option.\nBLAST+ 2.8.0: March 28, 2018\nNOTE: This is an alpha release to allow users to test and comment on new features\nImprovements\nSupport for a new version of the BLAST database that allows you to limit search by taxonomy as well some other improvements. See description at https://ftp.ncbi.nlm.nih.gov/blast/db/v5/blastdbv5.pdf .\nThe 2GB output file size limit for makeblastdb has been increased to 4 GB.\nBug fixes\nFix makeblastdb problem with producing spurious files with masking information.\nFix a problem with being unable to retrieve taxonomy information for tabular output.\nBLAST+ 2.7.1: October 23, 2017\nImprovements\nProvided an upper limit on the number of threads for BLAST+ search applications.\nImproved performance of taxonomic name lookups.\nFixed Mac installers so they are interoperable with other NCBI applications.\nReduced the amount of locking in BLASTDB reading library (CSeqDB).\nBug fixes\nFixed race condition when using gilist parameter.\nFixed culling_limit bug with HSPs from different strands\nFixed dustmasker bug with long region of Ns\nFixed bl2seq problem with HTML output\nNote: If building BLAST+ from source code, the LMDB library will be needed.\nBLAST+ 2.6.0: January 09, 2017\nNew features\nHandle bare accessions on blastdb_aliastool.\nChange defaults for output formats 6, 7, and 10 to incorporate version in accessions.\nImprovements\nAdd support for NCBI_DONT_USE_LOCAL_CONFIG and NCBI_DONT_USE_NCBIRC environment variables.\nBetter runtime performance in blastdbcmd when the entry_batch parameter is used.\nSAM output improvements.\nChanged gapped alignment starting point to minimize the chance to produce sub-optimal alignments.\nFor custom matrices absent from the util/tables source file, use BLOSUM62 for reporting number of positives.\nAdded long_seqids flag to blastdbcmd to use long (legacy) NCBI Seq-id format.\nBug fixes\nFixed issue with missing alignments in blastx.\nFixed problem processing accession.version in makeblastdb.\nFixed blastdbcmd problem with local IDs.\nRemoved memory leak for multi-threaded runs.\nFixed blastdbcmd crash when listing all entries and a sequence has no title.\nBLAST+ 2.5.0: September 12, 2016\nNew features\nComposition based statistics for rpstblastn.\nAdded output format for taxonomic organism report.\nSupport for bare accessions in FASTA and BLAST reports.\nImprovements\n-remote option connects to NCBI via HTTPS. This adds a dependency on GNUTLS (see https://www.ncbi.nlm.nih.gov/books/NBK279690/)\nPre-fetch sequences for formatting.\nBug fixes\nFixed improper functioning of output format 6 tokens ssciname, staxid, sscinames and staxids.\ntblastn core-dumps in multi-threaded mode.\nEnsure stable sorting of results in multi-threaded mode.\nFixed incorrect percent identity in tabular format for sequences containing selenocysteine.\nBLAST+ 2.4.0: June 02, 2016\nNew features\nIntroduced multi-threaded traceback for blastp, blastx, tblastn and tblastx.\nAdded new tabular format specifiers for taxonomic information (staxid, ssciname, scomname, sblastname, skingdom) that correspond to the first subject ID.\nImprovements\nSpeed up makeblastdb runtime performance with input consisting of many ambiguities.\nBetter support for 'bare' IDs in taxid_map option to makeblastdb.\nScore U (selenocysteine) as C (not X) in protein-protein and translated searches.\nBug fixes\nCorrected E-value computation in finite-size correction.\nRemoved memory leak from rpsblast.\nMade handling of ambiguities in subjects identical when using FASTA and BLAST database inputs.\nmakeblastdb no longer replaces tabs in definition line by '#'.\nCorrected problem with spaces in database names on windows.\nCorrected handling of subject_loc.\nBLAST+ 2.3.0: December 21, 2015\nNew features\nAdded new PSIBLAST command line options to support saving PSSM and checkpoint files for each iteration and calculate checkpoint and PSSM for the last iteration.\nAdded unique subject sequence query coverage to tabular output.\nAdded support single file JSON and XML2 Blast output format.\nBeta release of SAM output format.\nTreat N subject sequences, entered with the -subject argument (bl2seq mode), as one search set rather than N sets.\nImprovements\nmakeblastdb ignores and warns users about empty sequences in input.\nBLAST+ only accepts \"obinary\" windowmasker files for performance reasons.\nBug fixes\nBest hits processing multi-threaded context.\nFixed memory leak when invoking composition based statistics with an argument of 2.\nReturn non-zero exit code when failing to write output file.\nUse relative paths in XInclude file for multi-file XML2 output format.\nFixed memory leak in blastx.\nFixed inconsistent XML2 output to standard output vs. file.\nFixed psiblast incorrectly processing large input MSA.\nFixed bug when running BLAST+ on windows with multiple threads.\nBLAST+ 2.2.31: May 18, 2015\nNew features\nAdded support for BLAST-XML2 specification.\nAdded support for JSON Blast output format.\nImprovements\nImproved adaptive batch size algorithm to better handle small databases.\nPreface error/warning message(s) with name of the application.\nAllow multiple deflines even without GIs.\nDownload more concise database information for -remote searches.\nBug fixes\nFixed problem with makeblastdb's -max_file_sz.\nReenabled support for word size 5 in tblastn.\nFixed memory initialization problems.\nUse score for sorting search results if evalue less than 1.0e-180.\nBLAST+ 2.2.30: October 6, 2014\nNew features\nAdded tblastn-fast, blastp-fast, and blastx-fast tasks. These tasks make use of longer words as described by Shiryev et al. in http://www.ncbi.nlm.nih.gov/pubmed/17921491.\nAdded new output option (outfmt 12) with Seq-Align in JSON.\nImprovements\nAdded new command line option qcov_hsp_perc that removes alignments below the specified query coverage.\nAdded option line_length for the printing of alignment lengths (outfmt 0-4).\nAdded larger gap penalties for PAM30 and PAM70 matrices.\npsiblast now accepts 0 for num_iterations to indicate iterating until convergence.\nrpsblast uses composition-based-statistics by default. Recover old behavior with \"-comp_based_stats F -seg yes\".\nImproved blastn multithreading performance for many queries with small databases.\nChanged cmdline option -sum_stats (formerly -sum_statistics) from flag to boolean.\nBug fixes\nFixed spurious messages when parsing FASTA input.\nFixed makeprofiledb handling of PSSMs created from multiple sequence alignment.\nFixed makeblastdb handling of '-' at the end of FASTA input.\nFixed windowmasker segmentation fault when the incorrect window size is provided.\nFixed problem with lower-case masking and large sequences.\nFixed makeblastdb segmentation fault on duplicate seqids.\nAllow specification of scoring matrices in lower case letters.\nFixed exit code when disk space is not available for the output file.\nFixed problem with using seqids list from -outfmt \"6 sseqid\" as input with \u2013seqidlist.\nFixed bug with culling_limit that excludes top hit.\nFixed bug with max_target_seqs not working with psiblast.\nBLAST+ 2.2.29: January 3, 2014\nImprovements\nImproved the criteria for segging subject sequences used in composition based statistics with protein and translated searches.\nImproved blastn batch query performance.\nImproved blastdbcmd performance when retrieving taxonomic data from the BLAST databases.\nblastdb_aliastool supports reading a list of BLASTDBs from a file.\nSource releases build optimized multi-threaded binaries by default.\nMulti-threaded traceback: provides performance improvement for nucleotide-nucleotide BLAST with large (>25k) queries.\nMade makeprofiledb error messages more user friendly.\nUngapped BLAST no longer uses sum statistics by default. Recover old behavior with -sum_statistics flag.\nImproved multithreading by better dividing the BLAST database among threads.\nBug fixes\nAllow update_blastdb.pl to work with databases containing more than 100 volumes.\nmakeblastdb provides error message when -parse_seqids is used and invalid FASTA is provided.\nASCII PSSM output for psiblast and deltablast displays two-digit scores in a more readable manner.\nFixed negative percent identity in tabular output format\nRemoved -num_threads option for binaries built without multi-threading.\nFixed deltablast failures when searching multiple queries against multiple subject sequences.\nFixed segmasker exception on example from BLAST cookbook.\nFixed bogus warning about indexed megablast when using import search strategies.\nFixed missing hits when running blastn with multiple queries, word size 7, large evalue, and no low complexity filtering.\nFixed handling of gaps in ASN.1 input.\nFixed Statistics_hsp-len value of 0 in XML output from blast_formatter.\nFixed incorrect query coverage computation when sequence range was specified.\nTabular output no longer ignores the -db_gencode argument.\nFixed missing query sequence data in BLAST archive when -parse_deflines and FASTA with gnl ID was provided.\nProduce one XML document from BLAST archive.\nRemoved 100 volume restriction in blastdb_aliastool -num_volumes.\nFixed caption for 'query coverage' in tabular output format.\nApproximate gapped alignment in blastp is turned on/off for each query individually.\nFixed query genetic code option.\nBLAST+ 2.2.28: March 19, 2013\nNew features\nComposition based statistics support in rpsblast\nSupport for query coverage, subject sequence title, and taxonomy data in custom tabular output format\nblastdbcmd support for batch subsequence retrieval\nImprovements\nAdaptive BATCH_SIZE\nPerform incremental XML output\nBug fixes\nFormatting of asterix character in XML output\nSegmentation fault on out-of-memory\nPrevented extension of alignment into Ns\nSegmentation fault in DeltaBLAST when used with -remote and -out_ascii_pssm\nReplace tabs with spaces in FASTA deflines\nblastdbcmd displaying internal sequence ID for databases built without -parse_seqid\nblastdbcmd not fetching sequence data for complete sequence ID and -target_only\nblastn missing a hit for small word sizes\nCrash in blastn when it fetches sequence data from Genbank\nDeltaBLAST returning no hits when used with -remote option and searching more than one query\nInitialization problems for indexed megablast\npsiblast problem using -import_search_strategy\nblast_formatter displaying empty query for DeltaBLAST RID\nmakeblastdb problem with ASN.1 input\ndustmasker errors with acclist and maskinfo_xml output formats\nblastx reporting of HSPs dependent on -max_target_seqs\npsiblast's display of number of queries in tabular output format\nblastx error when -ungapped and -comp_based_stats F are used\nBLAST+ 2.2.27: September 10, 2012\nNew features\nComposition-based statistics for blastx.\nAdded seedtop - a tool for searching for patterns in an input sequence or BLAST database.\nEnable remote DELTA-BLAST searches.\nImprovements\nRevamped controls for the number of alignments/descriptions so that they are specific to applicable output formats (see user manual for details).\nReduce memory usage for BLAST searches that involve (large) multiple queries.\nSpeed up start-up times for BLAST databases.\nDisplay of new statistical parameters have been added to the BLAST results.\nSpeed up runtime performance of tabular output formatting.\nImprove the placement of gaps in MegaBLAST\nBug fixes\nFixed formatting bug when GI input format is provided to blastn.\nFixed incorrect composition-statistics default for DELTA-BLAST.\nBug fixes in blast_formatter, blastdbcmd.\nAn asterix (stop-codon) in sequence was not rendered properly.\nThe Smith-Waterman option in blastp would cause seg filtering on the subject sequence even if the composition-based statistics were not being used.\nThe makeblastdb taxid_map option is broken.\nBLAST+ 2.2.26: January 31, 2012\nNew features\nMac 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.\nAdded DELTA-BLAST - a new tool for sensitive protein searches\nAdded makeprofiledb - a tool for creating a database for RPS-BLAST\nImprovements\nThe blast_formatter application can now format bl2seq RIDs.\nPSI-BLAST can produce archive format, blast_formatter can format that output.\nPSI-BLAST has two new options that work with multiple-sequence alignments: ignore_msa_master and msa_master_idx (see BLAST+ manual).\nmkmbindex can now create masked indices from a BLAST database and ASN.1 masking data.\nAn improved finite size correction is now used for blastp/blastx/tblastn/rpsblast.\nThe 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.\nThe blastdbcmd -range parameter now accepts a blank value for the second parameter to signify the end of a sequence (e.g., -range \"100-\")\nThere was a performance improvement for long database sequences in results with many matches.\nBug fixes\nThere was a blastn problem if subject_loc and lcase_masking were used together.\nThere was a problem with multi-threaded blastx if the query included a long (10,000+) sequence of N's.\nThe percent identity calculation was wrong if the best-hit algorithm was used.\nThere was a problem with the multiple BLAST database statistics report in XML format.\nMakeblastdb failed to return an error when input was not available.\nThe formatting option -outfmt \"7 nident\" always printed zero.\nThe search strategy was not properly saving the -db_soft_mask option.\nAn error message was emitted if there was a \"<\" in the query title.\nA problem reading lower-case masking from the query could cause a search to fail.\nBLAST+ 2.2.26: March 15, 2011\nNew features\nEnhanced documentation, includes simplified setup instructions, available at\n\nhttp://www.ncbi.nlm.nih.gov/books/NBK1762\n\nImprovements\nAdded support for hard-masking of BLAST databases.\nImprove performance of makeblastdb for FASTA input with large numbers of sequences, improve error checking.\nAllow Best Hit options and XML formatting for Blast2Sequences mode\nAllow multiple query sequences for psiblast.\nAllow specification of any multiple sequence alignment sequence as the master with the -in_msa psiblast argument.\nAdd an optional -input_type argument to makeblastdb.\nAdded support for query and subject length to tabular output.\nPerformance of -seqidlist argument improved.\nThe minimum of the number of descriptions and alignments is now used for tabular and\nXML output (consistent with the behavior of the older blastall applications).\nBug fixes\nMakeblastdb and blastdbcmd problems with parsing, storing, and retrieving sequence identifiers.\nMissing subject identifiers in tabular output.\nBlast_formatter ignoring -num_alignments and -num_descriptions\nBlast archive format could be saved incorrectly with multiple queries.\nBlast_formatter established an unneeded network connection.\nBlast_formatter did not save masking information correctly.\nRpstblastn might crash if searching many sequences.\nIndexed megablast would not run in multi-threaded mode.\nQuery title in the PSSM saved by psiblast was not being stored.\nPossible failure to run in multi-threaded mode with multiple queries or large database sequences.\nTblastn runs with database masking might miss matches.\nBLAST+ 2.2.24 bug fix release: October 30, 2010\nBug fixes\nImproved makeblastdb performance and taxid_map option\nFixed segmentation faults on blastn and megablast\nFixed truncated output for sequence input with extra spaces in the defline\nFixed problem with MacOSX binaries on MacOSX 10.5\nBLAST+ 2.2.24: August 2, 2010\nAdded support for BLAST Archive format (see BLAST+ user manual)\nAdded the blast_formatter application (see BLAST+ user manual)\nAdded support for translated subject soft masking in the BLAST databases\nAdded support for the BLAST Trace-back operations (btop) output format\nAdded command line options to blastdbcmd for listing available BLAST databases\nImproved performance of formatting of remote BLAST searches\nUse a consistent exit code for out of memory conditions\nFixed bug in indexed megablast with multiple space-separated BLAST databases\nFixed bugs in legacy_blast.pl, blastdbcmd, rpsblast, and makeblastdb\nFixed Windows installer for 64-bit installations\nBLAST+ 2.2.23: Feb 03, 2010\nBug fix for tabular output formatting involving BLAST databases that do not have parseable deflines.\nFixed problem displaying accessions in XML output format.\nPrevent collisions between queries and subject sequences with local identifiers.\nFixed megablast performance regression when used with query masking.\nFixed seg filtering failure for blastx and genomic sequences.\nImplemented saving search strategies in bl2seq mode.\nFixed bug in tabular output format with qseq, sseq, pident and ppos keywords.\nFixed bug with blastp-short task.\nFixed blastdbcmd retrieval of taxids for BLAST databases without GIs.\nAdded makeblastdb support for adding masking information to existing BLAST databases.\nBLAST+ 2.2.22 Internal bug fix release: November 02, 2009\nFix issue dealing with opening BLAST databases which contain references to a\nBLAST database specified with a relative path.\nPrevent collisions between queries and subject sequences with local identifiers\nBLAST+ 2.2.22: Sep 27, 2009\nAdded entrez_query command line option for restricting BLAST databases.\nAdded support for psi-tblastn to the tblastn command line application via the -in_pssm option.\nImproved documentation for subject masking feature in user manual.\nUser interface improvements to windowmasker.\nMade the specification of BLAST databases to resolve GIs/accessions configurable.\nupdate_blastdb.pl downloads and checks BLAST database MD5 checksum files.\nAllowing long words with blastp.\nAdded support for overriding megablast index when importing search strategy files.\nAdded support for best-hit algorithm parameters in strategy files.\nBug fixes in blastx and tblastn with genomic sequences, subject masking,\nblastdbcheck, and the SEG filtering algorithm.\nBLAST+ 2.2.21: May 27, 2009\nAdded support for Best-Hit algorithm.\nAdded support for -in_msa psiblast option.\nPerformance improvements and bug fixes to subject soft masking feature (note: the file format for the files containing the masking information has changed in a non-backwards compatible way).\nChanged command line option to specify single soft masking algorithm to mask\nBLAST databases from -mask_subjects to -db_soft_mask.\nMasked FASTA and subject masks can be obtained via blastdbcmd.\nImproved error messages when makeblastdb processes masking information.\nBug fixes in tabular output for translated searches.\nBug fixes to makeblastdb.\nBug fixes to search strategies and megablast.\nBug fixes to XML output.\nBug fixes and performance improvements to multi-threaded execution.\nBug fixes to lower case masking in blastx.\nBug fixes to ungapped searches.\nAdded support for smaller lookup tables for small queries.\nAdded support for partial sequence fetching during traceback.\nFixed the 2-hit algorithm so that no overlap between two hits is allowed.\nImplemented a new method to compute effective observations and new entropy-based method to compute column-specific pseudocounts in PSI-BLAST.\nRemote BLAST database data loader is used as a fallback if local BLAST databases cannot be found.\nBug fixes, improved error messages, and support for ASN.1 input in makeblastdb.\nBug fixes and performance improvements to subject masking feature.\nAdded the update_blastdb.pl script\nUpdated BLAST+ user manual with documentation about configuring BLAST, automatic resolution of sequence identifiers, and a description of how the BLAST databases are searched.\nBLAST+ 2.2.19: November 03, 2008\nMade sequence ID/title display uniform in sequence filtering applications.\nFixed incorrect display of filtering options in XML output.\nFixed handling of empty sequences in BLAST input.\nFixed negative strand handling for tblastn/tblastx.\nBLAST+ 2.2.18: October 14, 2008\nAdded update_blastdb.pl script to distribution of BLAST+ command line applications.\nChanged a few PSI-BLAST constants for pseudo-counts.\nBug fix in blastdbcmd to distinguish non-redundant sequence titles.\nBug fix to display BLAST database information remotely from outside NCBI for XML output.\nBLAST+ 2.2.17 internal release: September 24, 2008\nFix to prevent initial seed extension from going beyond context boundary.\nImprovements to reduce memory usage when query splitting is applied.\nPrint the accession and version for blastdbcmd's %a output format.\ngilists/negative gilists are not saved in search strategies or supported in remote blast searches.\nlegacy_blast.pl fixed for MacOSX, as well as extended support for megablast formatting options (-D, -f).\nEnhancements to Mac installer to add installation path to user's PATH.\nASN.1 output is now of type Seq-annot.\n-lcase_masking option now applies to subject sequences as well as queries.\nBug fix for creation of masked databases with non-redundant sequences that use a BLAST database as its data source.\nBug fix for merging masking locations.\nBLAST+ 2.2.16 internal release: August 21, 2008\nFirst internal release", "pairs": [], "interleaved": []} | |
| {"file": "helpblast_NBK1762/blast_glossary.nxml", "text": "A fixed procedure embodied in a computer program.\nThe process or result of matching up the nucleotide or amino acid residues of two or more biological sequences to achieve maximal levels of identity and, in the case of amino acid sequences, conservation, for the purpose of assessing the degree of similarity and the possibility of homology.\nResearch, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.\nThe bit score, S', is derived from the raw alignment score, S, taking the statistical properties of the scoring system into account. Because bit scores are normalized with respect to the scoring system, they can be used to compare alignment scores from different searches.\nBasic Local Alignment Search Tool (Altschul et al., 1990 & 1997) is a sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. The initial search is done for a word of length \"W\" that scores at least \"T\" when compared to the query using a substitution matrix. Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of \"S\". The \"T\" parameter dictates the speed and sensitivity of the search.\n\n\n\nA Blocks Substitution Matrix is a substitution scoring matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members. (Henikoff and Henikoff, 1992)\n\n\n\nThese are methods applied to protein BLAST searches that adjust the significance of alignment scores by taking into account the overall amino acid composition of the query and aligned database sequences. These methods provide more accurate statistics than those originally used in protein BLAST searches (Sch\u00e4ffer et al., 2001; Yu and Altschul, 2005). The conditional compositional score matrix adjustment method (Yu and Altschul, 2005) is used by default on the NCBI protein BLAST service.\nA change at a specific position of an amino acid or, less commonly, DNA sequence that preserves the physico-chemical properties of the original residue or achieves a positive score in the governing scoring matrix.\nA discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function.\nA program for filtering low complexity regions from nucleic acid sequences.\nThe Expectation value or Expect value represents the number of different alignments with scores equivalent to or better than S that is expected to occur in a database search by chance. The lower the E value, the more significant the score and the alignment.\nThe first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called \"words\". Initially, the scores of segments in which there are multiple word hits are calculated (\"init1\"). Later the scores of several segments may be summed to generate an \"initn\" score. An optimized alignment that includes gaps is shown in the output as \"opt\". The sensitivity and speed of the search are inversely related and controlled by the \"k-tup\" variable that specifies the size of a \"word\" (Pearson and Lipman, 1988).\nFiltering, also known as masking, removes regions of (nucleic acid or amino acid) sequence having characteristics that may lead to spurious high scores. See SEG and DUST.\nA space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment.\nThe alignment of two nucleic acid or protein sequences over their entire length.\nH is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high values of H short alignments can be distinguished by chance, whereas at lower H values a longer alignment may be necessary (Altschul, 1991).\nSimilarity attributed to descent from a common ancestor. Homologous biological components (genes, proteins, structures) are called homologs. See also orthologs and paralogs.\nA High-scoring Segment Pair (HSP) is a local alignment with no gaps that achieves one of the highest alignment scores in a given search.\nThe extent to which two (nucleotide or amino acid) sequences have the same residues at the same positions in an alignment, often expressed as a percentage.\nA statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for search space size. The value K is used in converting a raw score (S) to a bit score (S').\nA statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for scoring system. The value lambda is used in converting a raw score (S) to a bit score (S').\nThe alignment of a high-scoring region of two nucleic acid or protein sequences.\nA region of biased composition in nucleic acid and protein sequences. These include homopolymeric runs, short-period repeats, and subtler over representation of one or a few residues. The SEG program is used to mask or filter low complexity regions in amino acid queries. The DUST program is used to mask or filter such regions in nucleic acid queries.\nAlso known as filtering. The removal of repeated or low complexity regions from a sequence in order to improve the sensitivity of sequence similarity searches performed with that sequence.\nA short conserved region in a protein sequence. Motifs are frequently highly conserved parts of domains.\nAn alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/or ancestral residues are aligned in the same column. Clustal W (Thompson, Higgins, and Gibson, 1994) is an example of a popular multiple sequence alignment program. The NCBI COBALT tool also produces multiple alignments of protein sequences (Papadopoulos and Agarwala, 2007).\nAn alignment of two sequences with the highest possible score.\nHomologous biological components (genes, proteins, structures) in different species that arose from a single component present in the common ancestor of the species; orthologs may or may not have a similar function. Compare with paralogs.\n\n\n\nThe probability of a chance alignment occurring with a particular score or a better score in a database search. The p value is calculated by relating the observed alignment score, S, to the expected distribution of HSP scores from comparisons of random sequences of the same length and composition as the query to the database. The most highly significant P values will be those close to 0. P values and E values are different ways of representing the significance of the alignment.\nPercent Accepted Mutation (PAM) is unit introduced by Margaret Dayhoff and colleagues to quantify the amount of evolutionary change in a protein sequence. 1.0 PAM unit is the amount of evolution that will change, on average, 1% of amino acids in a protein sequence. A PAM(x) substitution matrix is a look-up table in which scores for each amino acid substitution have been calculated based on the frequency of that substitution in closely related proteins that have experienced a certain amount (x) of evolutionary divergence.\nHomologous biological components within a single species that arose by gene duplication. Compare with orthologs.\nPosition Hit Initiated BLAST (PHI-BLAST) is a variant of PSI-BLAST that can focus the alignment and construction of the PSSM around a motif, which must be present in the query sequence and is provided as input to the program. Only database sequences that contain the motif in context will be included in the results. See also PSSM.\nA table that lists the frequencies of each amino acid in each position of protein sequence alignment. Frequencies are calculated from multiple alignments of sequences containing a domain of interest. See also PSSM.\nSystematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in a sample.\nPosition-Specific Iterative BLAST (PSI-BLAST) is an iterative search using the protein BLAST algorithm. A profile is built after the initial search that is then used in subsequent searches. The process may be repeated, if desired, with new sequences found in each cycle used to refine the profile (Altschul et al., 1997).\nA Position-Specific Scoring Matrix (PSSM) is a profile that gives the log-odds score for finding a particular matching amino acid in a target sequence.\nThe input sequence (or other type of search term) to which all of the entries in a database are to be compared.\nThe score of an alignment, S, calculated as the sum of substitution and gap scores. Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap scores are typically calculated as the sum of G, the gap opening penalty and L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15) and a low value for L (1-2).\n\n\n\nThe extent to which nucleotide or protein sequences are related. Similarity between two sequences can be expressed as percent sequence identity and/or percent positive substitutions.\nA program for filtering low complexity regions in amino acid sequences (Wootton and Federhen, 1996). Residues that have been masked are represented as \"X\" in an alignment. SEG filtering is no longer the default in the NCBI blastp service because of the use of compositional adjustments to estimate BLAST statistics. See composition-based statistics.\n\n\n\nThe presence of a non-identical amino acid at a given position in an alignment. If the aligned residues have similar physico-chemical properties or have a positive score in the governing scoring matrix the substitution is said to be conservative.\nA scoring matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids. Such matrices are constructed by assembling a large and diverse sample of verified pairwise alignments of protein sequences. If the sample is large enough, the resulting matrices should reflect the true probabilities of mutations occurring through a period of evolution. The BLOSUM matrices are examples of substitution scoring matrices.\nAlso known as identity matrix. This is a scoring system in which only identical characters receive a positive score.", "pairs": [], "interleaved": []} | |
| {"file": "helpblast_NBK1762/introduction.nxml", "text": "The Basic Local Alignment Search Tool (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. PSI-BLAST produces a position-specific-scoring-matrix (PSSM) starting with a protein query, and then uses that PSSM to perform further searches. It is also possible to compare a protein or nucleotide query to a database of PSSM\u2019s. The NCBI supports a BLAST web page at blast.ncbi.nlm.nih.gov as well as a network service. The NCBI also distributes stand-alone BLAST applications for users who wish to run BLAST on their own machines or with their own databases. This document describes the stand-alone BLAST applications and will concentrate on the latest generation of such applications included in the BLAST+ package.\nThe first two sections of this document are \u201cquick start\u201d guides that address setting BLAST+ up under UNIX (including LINUX and MacOSX) and Windows. The third section is a more in-depth look at the BLAST+ applications. These documents are currently being revised and may change substantially in coming releases.", "pairs": [], "interleaved": []} | |