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Truncates the report to [integer] number of alignments. There is no warning when you
exceed this limit, so it’s generally a good idea to set
[integer] very high unless you’re inter-
ested only in the top hits.
Programs: blastn, tblastn
Sets the number of queries to concatenate in a single search. Concatenating queries acceler-
ates the search because the database is scanned just one time. This is the principle
underlying megablast, but the implementation is different in blastall.
This option is new in Version 2.2.6 and still experimental. The specified
[integer] must be
the number of sequences in the query file. If it’s less, only the first set of
sequences is used. Also, the output is very different than you would expect. All the query
names are listed, and then all the one-line summaries are given, followed by the align-
ments, and finally, one footer is produced for the whole report. Given this format, it’s very
difficult to discern which alignments belong to which query. This option should not be
used in its current implementation.
Identifies the database to search. [database] must already be formatted by formatdb.
BLAST looks for
[database] in the following order: the local directory, the BLASTDB envi-
ronment variable (Unix only), and finally, the location specified in the .ncbirc file.
You can merge multiple databases into a single virtual database by putting the individual
databases in quotes. For example, to merge the nt and est databases, use:
-d "nt est". You
can’t mix nucleotide and amino acid databases. The statistics reported are based on the
sizes of the combined databases. Virtual databases may exceed file size limits imposed by
the operating system.
Programs: tblastn, tblastx
The genetic code to use for translation of the database nucleotide sequence. See http://
www.ncbi.nlm.nih.gov/htbin-post/Taxonomy for updates.
1 Standard Nuclear Genetic Code
2 Vertebrate Mitochondrial
3 Yeast Mitochondrial
4 Mold, Protozoan, and Coelocoel Mitochondrial