July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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Chapter 13: NCBI-BLAST Reference
-Z [integer]
Default: 25
Programs: All
Sets the X3 dropoff value (in bits) for extensions but is bounded by the value for X2. It’s
generally not necessary to adjust this parameter.
formatdb Parameters
formatdb turns FASTA files into BLAST databases (ASN.1 format is also acceptable,
but because it isn’t commonly used, it isn’t covered in this book. You can find more
information about ASN.1 at http://www.ncbi.nlm.nih.gov/Sitemap/Summary/asn1.
html/). Chapter 11 discusses the typical methods for building BLAST databases and
examines the NCBI identifier syntax required for some aspects of formatdb and
blastall. Here are a few sample command lines:
formatdb -i protein_db
formatdb -p F -i nucleotide_db
zcat est*.gz | formatdb -p F -i stdin -o -n est -v 2000000000
The following reference lists the default value for each formatdb parameter.
-B [file]
Default: Optional
Specifies a binary GI output file. The advantage of using a binary GI file is that it’s smaller
than a corresponding text file and can be read directly into memory without being parsed.
See the
-F option.
To convert a text GI file to binary, use the following command:
formatdb -F text_gi_list -B binary_gi_list
-F [file]
Default: Optional
Specifies a GI file, either text or binary. This is used for creating ...
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