Table C2: [blastn application options. The blastn...]. - BLAST® Command Line Applications User Manual

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BLAST® Command Line Applications User Manual [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2008-.

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Table C2:

blastn application options. The blastn application searches a nucleotide query against nucleotide subject sequences or a nucleotide database. An option of type “flag” takes no arguments, but if present the argument is true. Four different tasks are supported: 1.) “megablast”, for very similar sequences (e.g, sequencing errors), 2.) “dc-megablast”, typically used for inter-species comparisons, 3.) “blastn”, the traditional program used for inter-species comparisons, 4.) “blastn-short”, optimized for sequences less than 30 nucleotides.

option	task(s)	type	default value	description and notes
word_size	megablast	integer	28	Length of initial exact match.
word_size	dc-megablast	integer	11	Number of matching nucleotides in initial match. dc-megablast allows non-consecutive letters to match.
word_size	blastn	integer	11	Length of initial exact match.
word_size	blastn-short	integer	7	Length of initial exact match.
gapopen	megablast	integer	0	Cost to open a gap. See appendix “BLASTN reward/penalty values”.
gapextend	megablast	integer	none	Cost to extend a gap. This default is a function of reward/penalty value. See appendix “BLASTN reward/penalty values”.
gapopen	blastn, blastn-short, dc-megablast	integer	5	Cost to open a gap. See appendix “BLASTN reward/penalty values”.
gapextend	blastn, blastn-short, dc-megablast	integer	2	Cost to extend a gap. See appendix “BLASTN reward/penalty values”.
reward	megablast	integer	1	Reward for a nucleotide match.
penalty	megablast	integer	-2	Penalty for a nucleotide mismatch.
reward	blastn, dc-megablast	integer	2	Reward for a nucleotide match.
penalty	blastn, dc-megablast	integer	-3	Penalty for a nucleotide mismatch.
reward	blastn-short	integer	1	Reward for a nucleotide match.
penalty	blastn-short	integer	-3	Penalty for a nucleotide mismatch.
strand	all	string	both	Query strand(s) to search against database/subject. Choice of both, minus, or plus.
dust	all	string	20 64 1	Filter query sequence with dust.
filtering_db	all	string	none	Mask query using the sequences in this database.
window_masker_taxid	all	integer	none	Enable WindowMasker filtering using a Taxonomic ID.
window_masker_db	all	string	none	Enable WindowMasker filtering using this file.
soft_masking	all	boolean	true	Apply filtering locations as soft masks (i.e., only for finding initial matches).
lcase_masking	all	flag	N/A	Use lower case filtering in query and subject sequence(s).
db_soft_mask	all	integer	none	Filtering algorithm ID to apply to the BLAST database as soft mask (i.e., only for finding initial matches).
db_hard_mask	all	integer	none	Filtering algorithm ID to apply to the BLAST database as hard mask (i.e., sequence is masked for all phases of search).
perc_identity	all	integer	0	Percent identity cutoff.
template_type	dc-megablast	string	coding	Discontiguous MegaBLAST template type. Allowed values are coding, optimal and coding_and_optimal.
template_length	dc-megablast	integer	18	Discontiguous MegaBLAST template length.
use_index	megablast	boolean	false	Use MegaBLAST database index. Indices may be created with the makembindex application.
index_name	megablast	string	none	MegaBLAST database index name.
xdrop_ungap	all	real	20	Heuristic value (in bits) for ungapped extensions.
xdrop_gap	all	real	30	Heuristic value (in bits) for preliminary gapped extensions.
xdrop_gap_final	all	real	100	Heuristic value (in bits) for final gapped alignment.
no_greedy	megablast	flag	N/A	Use non-greedy dynamic programming extension.
min_raw_gapped_score	all	integer	none	Minimum raw gapped score to keep an alignment in the preliminary gapped and trace-back stages. Normally set based upon expect value.
ungapped	all	flag	N/A	Perform ungapped alignment.
window_size	dc-megablast	integer	40	Multiple hits window size, use 0 to specify 1-hit algorithm

From: Appendices

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