formatdb

formatdb

formatdb is used to format protein or nucleotide source databases before these databases can be searched by blastall, blastpgp or MegaBLAST.

An example of a formatdb command-line entry:

formatdb -i fastafile -p F -oflat file T

The following table summarizes the formatdb options.

Option

Definition

Type

Default

-a

Input file is database in ASN.1 format (otherwise FASTA is expected).

[T/F]

F

-b

ASN.1 database in binary mode:

T = Binary.
F = Text mode.

[T/F]

F

-e

Input is a Seq-entry.

[T/F]

F

-i

Input file for formatting (this parameter must be set).

[File In]

 

-l

Logfile name.

[File Out]

formatdb.log

-n

Base name for BLAST files.

[String]

 

-o

Parse options:

T = True: Parse SeqId and create indexes.
F = False: Do not parse SeqId. Do not create indexes.

[T/F]

F

-p

Type of file:

T = Protein.
F = Nucleotide.

[T/F]

T

-s

Create indexes limited only to accessions - sparse.

[T/F]

F

-t

Title for database file.

[String]

 

-v

Number of sequence bases to be created in the volume.

[Integer]

0

-A

Create ASN.1 structured deflines.

[T/F]

F

-B

Binary GIfile produced from the GIfile.

This option should be used with the -F option.

[File Out]

 

-F

GIfile (file containing list of GIs).

[File In]

 

-L

Create an alias file with this name.

[File Out]

 



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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