--- name: "blastall" section: "1" platform: "linux" package: "blast2" version: "1:2.2.26.20120620-8" release: "Debian 8 (Jessie)" platforms: ["linux"] url: "https://new.carta.tech/blast" --- # blastall(1) Basic Local Alignment Search Tool Part of [blast(1)](/blast/1.md). ## NAME bl2seq, blast2, blastall, blastall\_old, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop - Basic Local Alignment Search Tool ## SYNOPSIS **bl2seq** \[**-**\] \[**-A**\] \[**-D** *N*\] \[**-E** *N*\] \[**-F** *str*\] \[**-G** *N*\] \[**-I** "*start stop*"\] \[**-J** "*start stop*"\] \[**-M** *str*\] \[**-S** *N*\] \[**-T**\] \[**-U**\] \[**-V**\] \[**-W** *N*\] \[**-X** *N*\] \[**-Y** *X*\] \[**-a** *filename*\] \[**-d** *N*\] \[**-e** *X*\] \[**-g F**\] **-i** *filename* **-j** *filename* \[**-m**\] \[**-o** *filename*\] **-p** *str* \[**-q** *N*\] \[**-r** *N*\] \[**-t** *N*\] **blast2** \[**-**\] \[**-B** *N*\] \[**-D** *N*\] \[**-C** *x*\] \[**-E** *N*\] \[**-F** *str*\] \[**-G** *N*\] \[**-H**\] \[**-I** "*start stop*"\] \[**-J** "*start stop*"\] \[**-K** *N*\] \[**-L**\] \[**-M** *str*\] \[**-N**\] \[**-P** *X*\] \[**-Q** *N*\] \[**-R**\] \[**-S** *N*\] \[**-T** *N*\] \[**-W** *N*\] \[**-X** *N*\] \[**-Y** *X*\] \[**-Z** *N*\] \[**-a** *N*\] \[**-b** *N*\] \[**-c**\] \[**-d** *str*\] \[**-e** *X*\] \[**-f** *X*\] \[**-g**\] \[**-h** *N*\] \[**-i** *filename*\] \[**-j** *filename*\] \[**-k** *str*\] \[**-m** *N*\] \[**-n**\] \[**-o** *filename*\] **-p** *str* \[**-q** *N*\] \[**-r** *N*\] \[**-s\]** **\[-t** *N***\]** **\[-u\]** **\[-v** *N***\]** **\[-w** *N***\]** **\[-y** *N***\]** **\[-z** *N***\]** **blastall** **\[-\]** **\[-A** *N***\]** **\[-B** *N***\]** **\[-C** *x***\]** **\[-D** *N***\]** **\[-E** *N***\]** **\[-F** *str***\]** **\[-G** *N***\]** **\[-I\]** **\[-J\]** **\[-K** *N***\]** **\[-L** *start,stop***\]** **\[-M** *str***\]** **\[-O** *filename***\]** **\[-P** *N***\]** **\[-Q** *N***\]** **\[-R** *filename***\]** **\[-S\]** **\[-T\]** **\[-U\]** **\[-V\]** **\[-W** *N***\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f** *X***\]** **\[-g F\]** **\[-i** *filename***\]** **\[-l** *str***\]** **\[-m** *N***\]** **\[-n\]** **\[-o** *filename***\]** **-p** *str* **\[-q** *N***\]** **\[-r** *N***\]** **\[-s\]** **\[-t** *N***\]** **\[-v** *N***\]** **\[-w** *N***\]** **\[-y** *X***\]** **\[-z** *X***\]** **blastall\_old** **\[-\]** **\[-A** *N***\]** **\[-B** *N***\]** **\[-C** *x***\]** **\[-D** *N***\]** **\[-E** *N***\]** **\[-F** *str***\]** **\[-G** *N***\]** **\[-I\]** **\[-J\]** **\[-K** *N***\]** **\[-L** *start,stop***\]** **\[-M** *str***\]** **\[-O** *filename***\]** **\[-P** *N***\]** **\[-Q** *N***\]** **\[-R** *filename***\]** **\[-S\]** **\[-T\]** **\[-U\]** **\[-W** *N***\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f** *X***\]** **\[-g F\]** **\[-i** *filename***\]** **\[-l** *str***\]** **\[-m** *N***\]** **\[-n\]** **\[-o** *filename***\]** **-p** *str* **\[-q** *N***\]** **\[-r** *N***\]** **\[-s\]** **\[-t** *N***\]** **\[-v** *N***\]** **\[-w** *N***\]** **\[-y** *X***\]** **\[-z** *X***\]** **blastcl3** **\[-\]** **\[-A** *N***\]** **\[-C** *x***\]** **\[-D** *N***\]** **\[-E** *N***\]** **\[-F** *str***\]** **\[-G** *N***\]** **\[-I\]** **\[-J\]** **\[-K** *N***\]** **\[-L** *start,stop***\]** **\[-M** *str***\]** **\[-O** *filename***\]** **\[-Q** *N***\]** **\[-R\]** **\[-S\]** **\[-T\]** **\[-U\]** **\[-W** *N***\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f** *X***\]** **\[-g F\]** **\[-i** *filename***\]** **\[-m** *N***\]** **\[-n\]** **\[-o** *filename***\]** **-p** *str* **\[-q** *N***\]** **\[-r** *N***\]** **\[-s\]** **\[-t** *N***\]** **\[-u** *str***\]** **\[-v** *N***\]** **\[-w** *N***\]** **\[-y** *X***\]** **\[-z** *X***\]** **blastpgp** **\[-\]** **\[-A** *N***\]** **\[-B** *filename***\]** **\[-C** *filename***\]** **\[-E** *N***\]** **\[-F T\]** **\[-G** *N***\]** **\[-H** *N***\]** **\[-I\]** **\[-J\]** **\[-K** *N***\]** **\[-L** *N***\]** **\[-M** *str***\]** **\[-N** *X***\]** **\[-O** *filename***\]** **\[-P** *N***\]** **\[-Q** *filename***\]** **\[-R** *filename***\]** **\[-S** *N***\]** **\[-T\]** **\[-U\]** **\[-W** *N***\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-c** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f** *N***\]** **\[-h** *X***\]** **\[-i** *filename***\]** **\[-j** *N***\]** **\[-k** *filename***\]** **\[-l** *str***\]** **\[-m** *N***\]** **\[-o** *filename***\]** **\[-p** *str***\]** **\[-q** *N***\]** **\[-s\]** **\[-t** *N***\[u\]\]** **\[-u** *N***\]** **\[-v** *N***\]** **\[-y** *X***\]** **\[-z** *N***\]** **impala** **\[-\]** **\[-E** *N***\]** **\[-F** *str***\]** **\[-G** *N***\]** **\[-H\]** **\[-I\]** **\[-J\]** **\[-M** *str***\]** **\[-O** *filename***\]** **\[-P** *filename***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-c** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-h** *X***\]** **\[-i** *filename***\]** **\[-j** *N***\]** **\[-m** *N***\]** **\[-o** *filename***\]** **\[-v** *N***\]** **\[-y** *X***\]** **\[-z** *N***\]** **megablast** **\[-\]** **\[-A** *N***\]** **\[-D** *N***\]** **\[-E** *N***\]** **\[-F** *str***\]** **\[-G** *N***\]** **\[-H** *N***\]** **\[-I\]** **\[-J\]** **\[-L** *start,stop***\]** **\[-M** *N***\]** **\[-N** *N***\]** **\[-O** *filename***\]** **\[-P** *N***\]** **\[-Q** *filename***\]** **\[-R\]** **\[-S** *N***\]** **\[-T\]** **\[-U\]** **\[-V\]** **\[-W** *N***\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f\]** **\[-g F\]** **\[-i** *filename***\]** **\[-l** *str***\]** **\[-m** *N***\]** **\[-n\]** **\[-o** *filename***\]** **\[-p** *X***\]** **\[-q** *N***\]** **\[-r** *N***\]** **\[-t** *N***\]** **\[-s** *N***\]** **\[-v** *N***\]** **\[-y** *N***\]** **\[-z** *X***\]** **rpsblast** **\[-\]** **\[-F** *str***\]** **\[-I\]** **\[-J\]** **\[-L** *start,stop***\]** **\[-N** *X***\]** **\[-O** *filename***\]** **\[-P** *N***\]** **\[-T\]** **\[-U\]** **\[-X** *N***\]** **\[-Y** *X***\]** **\[-Z** *N***\]** **\[-a** *N***\]** **\[-b** *N***\]** **-d** *filename* **\[-e** *X***\]** **\[-i** *filename***\]** **\[-l** *filename***\]** **\[-m** *N***\]** **\[-o** *filename***\]** **\[-p F\]** **\[-v** *N***\]** **\[-y** *X***\]** **\[-z** *N***\]** **seedtop** **\[-\]** **\[-C** *N***\]** **\[-D** *N***\]** **\[-E** *N***\]** **\[-F\]** **\[-G** *N***\]** **\[-I\]** **\[-J\]** **\[-K** *N***\]** **\[-M** *str***\]** **\[-O** *filename***\]** **\[-S** *N***\]** **\[-X** *N***\]** **\[-d** *str***\]** **\[-e** *X***\]** **\[-f\]** **\[-i** *filename***\]** **\[-k** *filename***\]** **\[-o** *filename***\]** **\[-p** *str***\]** **\[-q** *N***\]** **\[-r** *N***\]** ## DESCRIPTION **This manual page documents briefly the commands bl2seq, blast,** **blastall, blastcl3, blastpgp, impala,** **megablast, rpsblast, and seedtop. These commands** **are documented together because they have a lot of common options.** **bl2seq performs a comparison between two sequences using either** **the blastn or blastp algorithm. Both sequences must be either** **nucleotides or proteins.** **blast2 compares a sequence against either a local database or a** **second sequence; it incorporates most of the functionality of both** **bl2seq and blastall, but uses a semi-experimental new** **internal engine.** **blastall and blastall\_old find the best matches in a** **local database for a sequence.** **blastall uses a newer engine than blastall\_old by default,** **but supports using the older engine as well (when invoked with the** **option -V F).** **blastcl3 accesses the newest NCBI BLAST search engine (version** **2.0). The software behind BLAST version 2.0 was written from scratch** **to allow BLAST to handle the new challenges posed by the sequence** **databases in the coming years. Updates to this software will continue** **in the coming years.** **blastpgp performs gapped blastp searches and can be used to** **perform iterative searches in psi-blast and phi-blast mode.** **impala searches a database of score matrices, prepared by** **[copymat(1)](/copymat/1.md), producing BLAST-like output.** **megablast uses the greedy algorithm of Webb Miller et al. for** **nucleotide sequence alignment search and concatenates many queries to** **save time spent scanning the database. This program is optimized for** **aligning sequences that differ slightly as a result of sequencing or** **other similar "errors". It is up to 10 times faster than more common** **sequence similarity programs and therefore can be used to swiftly** **compare two large sets of sequences against each other.** **rpsblast (Reverse PSI-BLAST) searches a query sequence against a** **database of profiles. This is the opposite of PSI-BLAST that searches** **a profile against a database of sequences, hence the \`Reverse'.** **rpsblast uses a BLAST-like algorithm, finding single- or** **double-word hits and then performing an ungapped extension on these** **candidate matches. If a sufficiently high-scoring ungapped alignment** **is produced, a gapped extension is performed and those (gapped)** **alignments with sufficiently low expect value are reported. This** **procedure is in contrast to IMPALA that performs a Smith-Waterman** **calculation between the query and each profile, rather than using a** **word-hit approach to identify matches that should be extended.** **seedtop answers two relatively simple questions:** - 1\. **Given a sequence and a database of patterns, which patterns occur** **in the sequence and where?** - 2\. **Given a pattern and a sequence database, which sequences contain the** **pattern and where?** **Some of these commands support multiple types of comparison, governed** **by the -p ("program") flag:** - blastp **compares an amino acid query sequence against a protein sequence** **database.** - blastn **compares a nucleotide query sequence against a nucleotide sequence** **database.** - blastx **compares the six-frame conceptual translation products of a nucleotide** **query sequence (both strands) against a protein sequence database.** **For bl2seq, the nucleotide should be the first sequence given.** - psitblastn **compares a protein query sequence against a nucleotide sequence** **database dynamically translated in all six reading frames (both** **strands) using a position specific matrix created by PSI-BLAST.** - tblastn **compares a protein query sequence against a nucleotide sequence** **database dynamically translated in all six reading frames (both** **strands). For bl2seq, the nucleotide should be the second** **sequence given.** - tblastx **compares the six-frame translations of a nucleotide query sequence** **against the six-frame translations of a nucleotide sequence database.** ## OPTIONS **A summary of options is included below.** - **-** **Print usage message** - **-A (bl2seq)** **Input sequences in the form of accession.version** - **-A** *N* **(blastall, blastall\_old, blastcl3, blastpgp, megablast)** **Multiple Hits window size; generally defaults to 0 (for single-hit** **extensions), but defaults to 40 when using discontiguous templates.** - **-B** *N* **(blast2)** **Produce on-the-fly output:** - 0 **none (default)** - 1 **table of offsets and quality values** - 2 **add sequence data** - 3 **text ASN.1** - 4 **binary ASN.1** - **-B** *N* **(blastall, blastall\_old)** **Number of concatenated queries, in blastn or tblastn mode** - **-B** *filename* **(blastpgp)** **Input Alignment File for PSI-BLAST Restart** - **-C** *X* **(blast2, blastall, blastall\_old, blastcl3)** **Use composition-based statistics for blastp or tblastn:** - T, t, D, or d **Default (equivalent to 1 for blast2 and blastall\_old** **and to 2 for blastall and blastcl3)** - 0, F, or f **No composition-based statistics** - 1 **Composition-based statistics as in** *NAR* **29:2994-3005, 2001** - 2 **Composition-based score adjustment as in** *Bioinformatics* **21:902-911,** **2005, conditioned on sequence properties** - 3 **Composition-based score adjustment as in** *Bioinformatics* **21:902-911,** **2005, unconditionally** **When enabling statistics in blastall, blastall\_old, or blastcl3 (***i.e.***,** **not blast2), appending u (case-insensitive) to the mode enables** **use of unified p-values combining alignment and compositional p-values** **in round 1 only.** - **-C** *filename* **(blastpgp)** **Output File for PSI-BLAST Checkpointing** - **-C** *N* **(seedtop)** **Score only or not (default = 1)** - **-D** *N* **(bl2seq)** **Output format:** - 0 **traditional (default)** - 1 **tabular** - **-D** *N* **(blast2, blastall, blastall\_old, blastcl3)** **Translate sequences in the database according to genetic code** *N* **in /usr/share/ncbi/data/gc.prt (default is 1; only applies to tblast\*)** - **-D** *N* **(megablast)** **Type of output:** - 0 **alignment endpoints and score** - 1 **all ungapped segments endpoints** - 2 **traditional BLAST output (default)** - 3 **tab-delimited one line format** - 4 **incremental text ASN.1** - 5 **incremental binary ASN.1** - **-D** *N* **(seedtop)** **Cost decline to align (default = 99999)** - **-E** *N* **(bl2seq, blastcl3, megablast)** **Extending a gap costs** *N* **(-1 invokes default behavior)** - **-E** *N* **(blast2, blastall, blastall\_old)** **Extending a gap costs** *N* **(-1 invokes default behavior:** **non-affine if greedy, 2 otherwise)** - **-E** *N* **(blastpgp, impala, seedtop)** **Extending a gap costs** *N* **(default is 1)** - **-F** *str* **(bl2seq, blast2, blastall, blastall\_old, blastpgp,** **blastcl3, impala, megablast, rpsblast)** **Filter options for DUST or SEG; defaults to T for bl2seq,** **blast2, blastall, blastall\_old, blastcl3, and megablast, and to** **F for blastpgp, impala, and rpsblast.** - **-F (seedtop)** **Filter sequence with SEG.** - **-G** *N* **(bl2seq, blastcl3, megablast)** **Opening a gap costs** *N* **(-1 invokes default behavior)** - **-G** *N* **(blast2, blastall, blastall\_old)** **Opening a gap costs** *N* **(-1 invokes default behavior: non-affine** **if greedy, 5 if using dynamic programming)** - **-G** *N* **(blastpgp, impala, seedtop)** **Opening a gap costs** *N* **(default is 11)** - **-H (blast2)** **Produce HTML output** - **-H** *N* **(blastpgp)** **End of required region in query (-1 indicates end of query)** - **-H (impala)** **Print help (different from usage message)** - **-H** *N* **(megablast)** **Maximal number of HSPs to save per database sequence (default is 0, unlimited)** - **-I "***start stop***" (bl2seq, blast2)** **Location on first (query) sequence (applies only if file specified** **with -i contains a single sequence)** - **-I (blastall, blastall\_old, blastcl3, blastpgp, impala, megablast,** **rpsblast, seedtop)** **Show GIs in deflines** - **-J "***start stop***" (bl2seq, blast2)** **Location on second (subject) sequence (applies only if file specified** **with -j contains a single sequence)** - **-J (blastall, blastall\_old, blastcl3, blastpgp, impala, megablast,** **rpsblast, seedtop)** **Believe the query defline** - **-K** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp)** **Number of best hits from a region to keep.** **Off by default.** **If used a value of 100 is recommended.** **Very high values of -v or -b are also suggested.** - **-K** *N* **(seedtop)** **Internal hit buffer size multiplier (wrt query length; default = 2)** - **-L (blast2)** **Use (classical Mega BLAST) lookup table with width 12** - **-L** *start,stop* **(blastall, blastall\_old, blastcl3, megablast,** **rpsblast)** **Location on query sequence (for rpsblast, only valid in blastp mode)** - **-M** *str* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **blastpgp, impala, seedtop)** **Use matrix** *str* **(default = BLOSUM62)** - **-M** *N* **(megablast)** **Maximal total length of queries for a single search (default = 5000000)** - **-N (blast2)** **Show only accessions for sequence IDs in tabular output** - **-N** *X* **(blastpgp, rpsblast)** **Number of bits to trigger gapping (default = 22.0)** - **-N** *N* **(megablast)** **Type of a discontiguous word template:** - 0 **coding (default)** - 1 **optimal** - 2 **two simultaneous** - **-O** *filename* **(blastall, blastall\_old, blastcl3,** **blastpgp, impala, megablast, rpsblast, seedtop)** **Write (ASN.1) sequence alignments to** *filename***; only valid for** **blastpgp, impala, rpsblast, and seedtop with -J, and only valid** **for megablast with -D2.** - **-P** *X* **(blast2)** **Identity percentage cut-off** - **-P** *N* **(blastall, blastall\_old, blastcl3, blastpgp, rpsblast)** **Set to 1 for single-hit mode or 0 for multiple-hit mode (default).** **Does not apply to blastn.** - **-P** *filename* **(impala)** **Read matrix profiles from database** *filename* - **-P** *N* **(megablast)** **Maximal number of positions for a hash value (set to 0 \[default\] to ignore)** - **-Q** *N* **(blast2, blastall, blastall\_old, blastcl3)** **Translate query according to genetic code** *N* **in** **/usr/share/ncbi/data/gc.prt (default is 1)** - **-Q** *filename* **(blastpgp)** **Output File for PSI-BLAST Matrix in ASCII** - **-Q** *filename* **(megablast)** **Masked query output; requires -D 2** - **-R (blast2)** **Compute locally optimal Smith-Waterman alignments.** **(This option is only available for gapped tblastn.)** - **-R** *filename* **(blastall, blastall\_old)** **Read PSI-TBLASTN checkpoint file** *filename* - **-R (blastcl3)** **RPS Blast search** - **-R** *filename* **(blastpgp)** **Input File for PSI-BLAST Restart** - **-R (megablast)** **Report the log information at the end of output** - **-S** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **megablast)** **Query strands to search against database for blastn, blastx, tblastx:** - 1 **top** - 2 **bottom** - 3 **both (default)** - **-S** *N* **(blastpgp)** **Start of required region in query (default = 1)** - **-S** *N* **(seedtop)** **Cutoff cost (default = 30)** - **-T (bl2seq, blastall, blastall\_old, blastcl3, blastpgp, megablast,** **rpsblast)** **Produce HTML output** - **-T** *N* **(blast2)** **Type of a discontiguous word template:** - 0 **coding (default)** - 1 **optimal** - 2 **two simultaneous** - **-U (bl2seq, blastall, blastall\_old, blastcl3, blastpgp, megablast,** **rpsblast)** **Use lower case filtering for the query sequence** - **-V (bl2seq, blastall, megablast)** **Force use of legacy engine** - **-V (blast2)** **Use variable word size approach to database scanning** - **-W** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **blastpgp, megablast, rpsblast)** **Use words of size** *N* **(length of best perfect match; zero invokes** **default behavior, except with megablast, which defaults to 28, and** **blastpgp, which defaults to 3. The default values for the other** **commands vary with "program": 11 for blastn, 28 for megablast, and 3** **for everything else.)** - **-X** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **blastpgp, megablast, rpsblast, seedtop)** **X dropoff value for gapped alignment (in bits) (zero invokes default** **behavior, except with megablast, which defaults to 20, and rpsblast** **and seedtop, which default to 15. The default values for the other** **commands vary with "program": 30 for blastn, 20 for megablast, 0 for** **tblastx, and 15 for everything else.)** - **-Y** *X* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **blastpgp, megablast, rpsblast)** **Effective length of the search space (use zero for the real size)** - **-Z** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **megablast, rpsblast)** **X dropoff value for final \[dynamic programming?\] gapped alignment in** **bits (default is 100 for blastn and megablast, 0 for tblastx, 25 for** **others)** - **-a** *filename* **(bl2seq)** **Write text ASN.1 output to** *filename* - **-a** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, megablast, rpsblast)** **Number of threads to use (default is one)** - **-b** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, megablast, rpsblast)** **Number of database sequences to show alignments for (B) (default is 250)** - **-c (blast2)** **Mask lower case** - **-c** *N* **(impala)** **Constant in pseudocounts for multipass version; 0 (default) uses** **entropy method; otherwise a value near 30 is recommended** - **-c** *N* **(impala)** **Constant in pseudocounts for multipass version (default is 10)** - **-d** *N* **(bl2seq)** **Use theoretical DB size of** *N* **(zero stands for the real size)** - **-d** *str* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, megablast, seedtop)** **Database to use (default is nr for all executables except blast2,** **which requires a second FASTA sequence if this is not set)** - **-d** *filename* **(rpsblast)** **RPS BLAST Database** - **-e** *X* **Expectation value (E) (default = 10.0)** - **-f** *X* **(blast2, blastall, blastall\_old, blastcl3)** **Threshold for extending hits, default if zero: 0 for blastn and** **megablast, 11 for blastp, 12 for blastx, and 13 for tblasn and** **tblastx.** - **-f** *N* **(blastpgp)** **Threshold for extending hits (default 11)** - **-f (megablast)** **Show full IDs in the output (default: only GIs or accessions)** - **-f (seedtop)** **Force searching for patterns even if they are too likely** - **-g F (bl2seq, blastall, blastall\_old, blastcl3)** **Do not perform gapped alignment (N/A for tblastx)** - **-g (blast2)** **Use greedy algorithm for gapped extensions** - **-g F (megablast)** **Make discontiguous megablast generate words for every base of the** **database (mandatory with the current BLAST engine)** - **-h** *N* **(blast2)** **Frame shift penalty for out-of-frame gapping (blastx, tblastn only;** **default is zero)** - **-h** *X* **(blastpgp, impala)** **e-value threshold for inclusion in multipass model (default = 0.002** **for blastpgp, 0.005 for impala)** - **-i** *filename* **Read (first, query) sequence or set from** *filename* **(default is** **stdin; not needed for blastpgp if restarting from scoremat)** - **-j** *filename* **(bl2seq, blast2)** **Read second (subject) sequence or set from** *filename* - **-j** *N* **(blastpgp)** **Maximum number of passes to use in multipass version (default = 1)** - **-k** *str* **(blast2)** **Pattern for PHI-BLAST** - **-k** *filename* **(blastpgp, seedtop)** **Input hit file for PHI-BLAST (default = hit\_file)** - **-l** *str* **(blastall, blastall\_old, blastpgp, megablast)** **Restrict search of database to list of GI's \[String\]** - **-l** *filename* **(rpsblast)** **Log messages to** *filename* **rather than standard error.** - **-m (bl2seq)** **Use Mega Blast for search** - **-m** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, megablast, rpsblast)** **alignment view options:** - 0 **pairwise (default)** - 1 **query-anchored showing identities** - 2 **query-anchored, no identities** - 3 **flat query-anchored, show identities** - 4 **flat query-anchored, no identities** - 5 **query-anchored, no identities and blunt ends** - 6 **flat query-anchored, no identities and blunt ends** - 7 **XML Blast output (not available for impala)** - 8 **tabular (not available for impala)** - 9 **tabular with comment lines (not available for impala)** - 10 **ASN.1 text (not available for impala or rpsblast)** - 11 **ASN.1 binary (not available for impala or rpsblast)** - **-n (blast2)** **Show GIs in sequence IDs** - **-n (blastall, blastall\_old, blastcl3)** **MegaBlast search** - **-n (megablast)** **Use non-greedy (dynamic programming) extension for affine gap scores** - **-o** *filename* **Write final alignment report to** *filename* **rather than stdout** - **-p** *str* **(bl2seq, blast2, blastall, blastall\_old, blastcl3)** **Use the "program" (comparison type)** *str***. The DESCRIPTION** **section covers this option in more detail.** - **-p** *str* **(blastpgp)** **program option for PHI-BLAST (default = blastpgp)** - **-p** *X* **(megablast)** **Identity percentage cut-off (default = 0)** - **-p F (rpsblast)** **Query sequence is nucleotide, not protein** - **-p** *str* **(seedtop)** **program name:** - patmatchp **indicates which patterns occur in a sequence** - patternp **indicates which sequences contain a pattern** - **-q** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **megablast, seedtop)** **Penalty for a nucleotide mismatch (blastn only) (default = -10 for** **seedtop, -3 for everything else)** - **-q** *N* **(blastpgp)** **ASN.1 Scoremat input of checkpoint data:** - 0 **no scoremat input (default)** - 1 **restart from ASCII scoremat checkpoint file** - 2 **restart from binary scoremat checkpoint file** - **-r** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3,** **megablast, seedtop)** **Reward for a nucleotide match (blastn only) (default = 10 for seedtop,** **-10 for everything else)** - **-s (blast2)** **No-op (formerly requested generating words for every base of the database)** - **-s (blastall, blastall\_old, blastcl3, blastpgp)** **Compute locally optimal Smith-Waterman alignments.** **For blastall, blastall\_old, and blastcl3, this is only available in gapped** **tblastn mode.** - **-s** *N* **(megablast)** **Minimal hit score to report (0 for default behavior)** - **-t** *N* **(bl2seq, blast2, blastall, blastall\_old, blastcl3)** **Length of a discontiguous word template (the largest intron allowed in** **a translated nucleotide sequence when linking multiple distinct** **assignments; default = 0; negative values disable linking for blastall,** **blastall\_old, and blastcl3.)** - **-t** *N***\[u\] (blastpgp)** **Composition-based score adjustment.** **The first character is interpreted as follows:** - 0, F, or f **no composition-based statistics** - 1 **composition-based statistics as in** *NAR* **29:2994-3005, 2001** - 2, T, or t **composition-based score adjustment as in** *Bioinformatics* **21:902-911, 2005, conditioned on sequence properties in round 1 (default)** - 3 **composition-based score adjustment as in** *Bioinformatics* **21:902-911, 2005, unconditionally in round 1** **When composition-based statistics are in use, appending u** **(case-insensitive) to the argument requests unified p-value combining** **alignment p-value and compositional p-value in round 1 only.** - **-t** *N* **(megablast)** **Length of a discontiguous word template (contiguous word if 0 \[default\])** - **-u (blast2)** **Do only ungapped alignment (always TRUE for tblastx)** - **-u** *str* **(blastcl3)** **Restrict search of database to results of Entrez2 lookup** - **-u** *N* **(blastpgp)** **ASN.1 Scoremat output of checkpoint data:** - 0 **no scoremat output (default)** - 1 **output ASCII scoremat checkpoint file (requires -J)** - 2 **output binary scoremat checkpoint file (requires -J)** - **-v** *N* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, megablast, rpsblast)** **Number of one-line descriptions to show (V) (default = 500)** - **-w** *N* **(blast2)** **Window size (max. allowed distance between a pair of initial hits; 0** **invokes default behavior, -1 turns off multiple hits)** - **-w** *N* **(blastall, blastall\_old, blastcl3)** **Frame shift penalty (OOF algorithm for blastx)** - **-y** *X* **(blast2, blastall, blastall\_old, blastcl3, blastpgp,** **impala, rpsblast)** **X dropoff for ungapped extensions in bits (0.0 invokes default** **behavior: 20 for blastn, 10 for megablast, and 7 for all others.)** - **-y** *N* **(megablast)** **X dropoff value for ungapped extension (default is 10)** - **-z** *N* **(blast2)** **Longest intron length for uneven gap HSP linking (tblastn only;** **default is 0)** - **-z** *N* **(blastall, blastall\_old, blastcl3, blastpgp, impala,** **megablast, rpsblast)** **Effective length of the database (use zero for the real size)** ## BUGS **This manual page is long and confusing; individual pages might be better.** ## AUTHOR **The National Center for Biotechnology Information.** ## SEE ALSO [**blastclust**(1)](/blastclust/1.md), [**copymat**(1)](/copymat/1.md), [**fastacmd**(1)](/fastacmd/1.md), [**formatdb**(1)](/formatdb/1.md), [**formatrpsdb**(1)](/formatrpsdb/1.md), [**makemat**(1)](/makemat/1.md), [**taxblast**(1)](/taxblast/1.md), **/usr/share/doc/blast2/blast.html,** **/usr/share/doc/blast2/seedtop.html,** **\.**