BlastnOptionalArguments

Location on the query sequence in 1-based offsets (Format: start-stop)

Task to execute, Permissible values: 'blastp' 'blastp-short' 'deltablast' Default = `blastp'

Word size for wordfinder algorithm, >=2

Cost to open a gap

Cost to extend a gap

Scoring matrix name (normally BLOSUM62)

Minimum word score such that the word is added to the BLAST lookup table, >=0

Use composition-based statistics: D or d: default (equivalent to 2 ) 0 or F or f: No composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : 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

Default = `2'

Location on the subject sequence in 1-based offsets (Format: start-stop)

• Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask, remote

Alignment view options: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = XML Blast output, 6 = tabular, 7 = tabular with comment lines, 8 = Text ASN.1, 9 = Binary ASN.1, 10 = Comma-separated values, 11 = BLAST archive format (ASN.1)

Options 6, 7, and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers. The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion qaccver means Query accesion.version qlen means Query sequence length sseqid means Subject Seq-id sallseqid means All subject Seq-id(s), separated by a ';' sgi means Subject GI sallgi means All subject GIs sacc means Subject accession saccver means Subject accession.version sallacc means All subject accessions slen means Subject sequence length qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a '/' qframe means Query frame sframe means Subject frame btop means Blast traceback operations (BTOP) staxids means Subject Taxonomy ID(s), separated by a ';' sscinames means Subject Scientific Name(s), separated by a ';' scomnames means Subject Common Name(s), separated by a ';' sblastnames means Subject Blast Name(s), separated by a ';' (in alphabetical order) sskingdoms means Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle means Subject Title salltitles means All Subject Title(s), separated by a sstrand means Subject Strand qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP When not provided, the default value is: 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore', which is equivalent to the keyword 'std' Default = `0'

Show NCBI GIs in deflines?

Number >=0 of database sequences to show one-line descriptions for Not applicable for outfmt > 4 Default = `500'

• Incompatible with: max_target_seqs

Number >=0 of database sequences to show alignments for Default = `250'

• Incompatible with: max_target_seqs

Produce HTML output?

Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = `no'

Apply filtering locations as soft masks Default = `false'

Use lower case filtering in query and subject sequence(s)?

Restrict search of database to list of GI's

• Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc

Restrict search of database to list of SeqId's

• Incompatible with: gilist, negative_gilist, remote, subject, subject_loc

Restrict search of database to everything except the listed GIs

• Incompatible with: gilist, seqidlist, remote, subject, subject_loc

Restrict search with the given Entrez query

• Requires: remote

Filtering algorithm ID to apply to the BLAST database as soft masking

• Incompatible with: db_hard_mask, subject, subject_loc

Filtering algorithm ID to apply to the BLAST database as hard masking

• Incompatible with: db_soft_mask, subject, subject_loc

If the query range of a hit is enveloped by that of at least this many higher-scoring hits >=0, delete the hit

• Incompatible with: best_hit_overhang, best_hit_score_edge

Best Hit algorithm overhang value ((0, 0.5), recommended value: 0.1)

• Incompatible with: culling_limit

Best Hit algorithm score edge value ((0, 0.5), recommended value: 0.1)

• Incompatible with: culling_limit

Maximum number >=1 of aligned sequences to keep Not applicable for outfmt less than 4 Default = `500'

• Incompatible with: num_descriptions, num_alignments

Effective length of the database

Effective length >=0 of the search space

Override maximum number >=0 of HSPs per subject to save for ungapped searches (0 means do not override) Default = `0'

Search strategy to use

• Incompatible with: export_search_strategy

File name to record the search strategy used

• Incompatible with: import_search_strategy

X-dropoff value (in bits) for ungapped extensions

X-dropoff value (in bits) for preliminary gapped extensions

X-dropoff value (in bits) for final gapped alignment

Multiple hits window size >=0, use 0 to specify 1-hit algorithm

Perform ungapped alignment only?

Should the query and subject defline(s) be parsed?

Number of threads >=1 (CPUs) to use in the BLAST search Default = `1'

• Incompatible with: remote

Execute search remotely?

• Incompatible with: gilist, seqidlist, negative_gilist, subject_loc, num_threads

Compute locally optimal Smith-Waterman alignments?

-query <File_In>

Input file name Default = `-'