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 an alias database that

doesn’t contain sequences, but pointers to sequences stored in another database (which

may be an alias database as well). See the

-L parameter. The databases must use the NCBI

FASTA identifier syntax, include GI numbers, and be indexed with

-o.

-i [file]

Default: Required

Sets the input FASTA file. You may specify that input come from stdin with -i stdin, but

you must also set the

-n parameter to give it a name. If you wish to make a single BLAST

database from multiple FASTA files, pipe them to formatdb as follows:

cat file1 file2 file3 | formatdb -i stdin -n my_db

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formatdb Parameters

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-l [file]

Default: formatdb.log

Specifies an output log file. Log messages are appended to this file.

-L [file]

Default: Optional

Creates an alias database, which has several uses. It can be a simple synonym for another

database, a selection of specific records from a database (see the

-F option), or a static

virtual database. Alias databases have the .pal or .nal extension, depending on whether they

are proteins or nucleotides.

To create an alias database with a selected set of GI numbers:

formatdb -i db -F gi_list -L alias_name -p [T/F]

To merge databases, first create a synonymous alias and then edit it to include additional

database names. Chapter 11 covers this process in more detail.

-n [string]

Default: Optional, required with -i stdin

Sets the base name for the BLAST database. If not specified, the name of the FASTA file

will be used. If the input is from stdin, this parameter must be set.

-o [T/F]

Default: Optional

Creates indexes. Indexing the databases isn’t required but is recommended. Alias data-

bases that use GI lists (see

-F and -L options) and the blastall -l option require indexed

databases. Additionally, some blastall output options specified with the

-m parameter

require indexing. Indexing adds four files with extensions .nnd, .nni, .nsd, and .nsi for

nucleotides and .pnd, .pni, .psd, and .psi for proteins. If you know you don’t need indexes,

you can save space by omitting

-o.

If GI numbers are included and more than one sequence has the same GI number,

formatdb terminates with an error. If accession numbers aren’t unique, an error won’t be

issued (see

-V).

-p [T/F]

Default: T

Specifies the type of type of file being formatted. By default, formatdb assumes the file is

protein, so you must set

-p F whenever you format nucleotide databases.