Formatdb README
------------------

Table of Contents

Introduction

Command Line Options

Formatdb Notes/Troubleshooting

A The -o option and identifiers
B "SORTFiles failed" message
C Formatting large FASTA files
D Piping a database to formatdb without uncompressing
E Creating custom databases.
F General troubleshooting tips.
G "SeqIdParse Failure" error
H "FileOpen" error

Appendix 1: The Files Produced by Formatdb

Introduction
------------
Formatdb must be used in order to format protein or nucleotide source
databases before these databases can be searched by blastall, blastpgp
or MegaBLAST. The source database may be in either FASTA or ASN.1
format. Although the FASTA format is most often used as input to
formatdb, the use of ASN.1 is advantageous for those who are using
ASN.1 as the common source for other formats such as the GenBank
report. Once a source database file has been formatted by formatdb it
is not needed by BLAST. Please note that if you are going to apply
periodic updates to your BLAST databases using fmerge
(ftp://ftp.ncbi.nih.gov/blast/fmerge/README), you will need to keep the
source database file.

If you are having problems formatting a BLAST databases please scroll
down to the "Formatdb Notes/Troubleshooting" section below. Or contact
the BLAST Desk at blast-help@ncbi.nlm.nih.gov

Command Line Options
--------------------
A list of the command line options for formatdb may be obtained by
executing formatdb without options, as in:

formatdb -

The formatdb options are summarized below:

formatdb arguments:

-t Title for database file [String]
Optional
-i Input file for formatting (this parameter must be set)
[File In]
-l Logfile name: [File Out]
Optional
default = formatdb.log
-p Type of file
T - protein
F - nucleotide [T/F] Optional
default = T

-o Parse options
T - True: Parse SeqId and create indexes.
F - False: Do not parse SeqId. Do not create indexes.
[T/F] Optional default = F

If the "-o" option is TRUE (and the source database is in FASTA
format), then the database identifiers in the FASTA definition
line must follow the convention of the FASTA Defline Format.
Please see section "F Note on creating custom databases"
below.

-a Input file is database in ASN.1 format (otherwise FASTA is expected)
T - True,
F - False.
[T/F] Optional default = F

-b ASN.1 database in binary mode
T - binary,
F - text mode.
[T/F] Optional default = F

A source ASN.1 database may be represented in two formats -
ascii text and binary. The "-b" option, if TRUE, specifies that
input ASN.1 database is in binary format. The option is ignored
in case of FASTA input database.

-e Input is a Seq-entry [T/F]
Optional
default = F

A source ASN.1 database (either text ascii or binary) may
contain a Bioseq-set or just one Bioseq. In the latter case the
"-e" switch should be set to TRUE.

-n Base name for BLAST files [String]
Optional

This options allows one to produce BLAST databases with a
different name than that of the original FASTA file. For
instance, one could have a file named 'ecoli.nuc.txt' and and
format it as 'ecoli':

formatdb -i ecoli.nuc.txt -p F -o T -n ecoli

uncompress -c nr.z | formatdb -i stdin -o T -n nr

This can be used in situations where the original FASTA file is
not required other than by formatdb. This can help in a
situation where disk-space is tight.

-v Number of sequence bases to be created in the volume
[Integer]
Optional
default = 0

This option breaks up large FASTA files into 'volumes' (each
with a maximum size of 2 billion letters). As part of the
creation of a volume formatdb writes a new type of BLAST
database file, called an alias file, with the extension 'nal'
or 'pal'.

-s Create indexes limited only to accessions - sparse [T/F]
Optional
default = F

This option limits the indices for the string identifiers (used
by formatdb) to accessions (i.e., no locus names). This is
especially useful for sequences sets like the EST's where the
accession and locus names are identical. Formatdb runs faster
and produces smaller temporary files if this option is used.
It is strongly recommended for EST's, STS's, GSS's, and
HTGS's.

-A Create ASN.1 structured deflines [T/F]
Optional
default = F

This option produces a new BLAST database format. The BLAST
programs can read this format as well as the current format.
The program automatically identifies which version it should work
with. This new format stores the sequence definition lines in
a structured manner (as ASN.1), this will allow future versions of
BLAST to better present taxonomic information as well as information
about other resources (e.g., UniGene, LocusLink) for a database sequence.

-L Create an alias file with this name
use the gifile arg (below) if set to calculate db size
use the BLAST db specified with -i (above) [File Out] Optional

This option produces a BLAST database alias file using a specified
database, but limiting the sequences searched to those in the GI list
given by the -F argument. See the section "Note on creating an alias file
for a GI list" for more information.

-F Gifile (file containing list of gi's) [File In] Optional

This option can be used to specify the GI list for the alias file
construction (-L option above) or to produce a binary GI list if
the -B option (below) is set.

-B Binary Gifile produced from the Gifile specified above [File Out] Optional

This option specifies the name of a binary GI list file. This option should
be used with the -F option. A text GI list may be specified with the -F
option and the -B option will produce that GI list in binary format. The
binary file is smaller and BLAST does not need to convert it, so it can
be read faster.

Formatdb Notes/Troubleshooting:
-------------------------------

A.) Note on -o option:

It is always advantageous to use the '-o' option if the database
identifiers are in the format specified at
ftp://ftp.ncbi.nih.gov/blast/db/README. If the database identifiers
are in this parseable format, formatdb produces additional indices
allowing retrieval from the databases by identifier. The databases on
the NCBI FTP site contain parseable identifiers. It is sufficient if
the first word on the FASTA definition line is a unique identifier
(e.g., ">3091 Alcoho de..."). It is necessary to use parseable
identifiers for the following cases:

1.) ASN.1 is to be produced from blastall or blastpgp, then "-o" must
be TRUE.

2.) query-anchored alignments are desired (i.e., the '-m' option with a
non-zero value is used).

3.) The gi's are desired as part of the output (i.e., '-I' is used).

4.) fastacmd will be used to fetch sequences from the database by
accession or gi.

See Appendix 1: The Files Produced by Formatdb for more information
in the -o T option.

B.) Note on "SORTFiles failed" message:

Formatdb will use the 'standard' temporary directory to sort the string
indices on disk. Under UNIX this directory is often /var/tmp and if
there is not enough space there, then the error message: "ERROR:
[000.000] SORTFiles failed" will be issued. This can be avoided by
setting the TMPDIR environment variable to a partition with more free
space. This message may also often be avoided by using the sparse
option (-s) for formatdb described above.

C.) Note on formatting large (4 Gig and larger) FASTA files:

A single BLAST database can contain up to 4 billion letters. If one
wishes to formatdb a FASTA file containing more letters than this, several
databases, each of a maximum size of 4 billion bases, will be produced.
This will be done automatically if the -v argument is not set. One may
also specify a smaller size for the volume databases by using the -v option:

formatdb -i hugefasta -p F -v 2000000000

This command line will format the "hugefasta" FASTA file as a number of
database "volumes," each containing a maximum of two billion base
pairs, as specified by the "-v" option. Two billion is the current
limitation on the NCBI toolkit command-line parser. The volumes will
have names consisting of the root database name, "hugefasta" followed
by a two-digit volume extension, followed by the usual BLAST database
extensions. These smaller databases can be searched as if they were a
single entity using:

blastall -i infile -d hugefasta -p blastn -o out

In this case, BLAST recognizes that the database "hugefasta" has been
partitioned into several volumes because it detects a file with the
name of the root database followed by an extension of "nal" (for
protein databases, the extension is "pal"). This file specifies a
database list to be searched when the root database name is specified
to BLAST. BLAST sequentially searches each database listed in this
"nal" file and generates output that is indistinguishable from that of
a single database search. A sample "nal" file, resulting from
formatting the datafile "hugefasta" into three volumes, is given below.
The "DBLIST" line can also be edited to specify additional databases to
be searched.

#
# Alias file created Tue Jan 18 13:12:24 2000
#
#
TITLE hugefasta
#
DBLIST hugefasta.00 hugefasta.01 hugefasta.02
#
#GILIST
#
#OIDLIST
#

The "nal" and "pal" files can also be used to simplify searches of
multiple databases created separately. For instance, a file called
"multi.nal" containing the following lines could be created from
scratch using a text editor.

#
# Alias file created Tue Jan 18 13:12:24 2000
#
#
TITLE multi
#
DBLIST part1 part2 part3
#
#GILIST
#
#OIDLIST
#

The "multi.nal" file would allow the three databases, "part1", "part2",
and "part3", to be searched by specifying a single database name,
"multi", on the blastall command line as follows:

blastall -i infile -d multi -p blastn -o out

The reason for using database volumes, as opposed to simply making the
indices in the BLAST databases large enough to handle all conceivable
databases with an eight-byte 'integer', is that this would have
doubled the size of the indices for all searches no matter how small
the database. Hence very large FASTA files are broken down into a
couple of databases.

Formatdb must be able to open files larger than 2 Gig in order to work
on very large files. This is not a problem on a 64-bit OS and on
certain 32-bit OS that allows binaries to be made large-file aware.
The 32-bit Solaris formatdb binary on the NCBI FTP site is now compiled
large file aware.

D.) Note on running formatdb on a database without uncompressing it:

Under UNIX it is possible to uncompress a database on the fly and pipe
it to formatdb. This can reduce the disk-space needed for running
formatdb on a large database. In addition, some operating systems
cannot write files larger than 2 Gig to disk. To circumvent this on
Unix or Linux systems, use a "pipe" system such as:

uncompress -c nt.Z|formatdb -i stdin -o T -p T -n "nt" -v 100000000

In this case, no file is written which is larger than 1 Gig and an
arbitrarily large database is formatted as a set of 1 Gig volumes.
Note the use of the '-n' option that specifies the name of the
resulting BLAST database. Note also that 'stdin' specifies that input
will be coming from 'standard input'. The nt FASTA file is not needed
for running BLAST searches and nt.Z may be deleted after formatdb has
been run.

E) Note on creating custom databases

With Standalone BLAST it is possible to take any custom file of FASTA
sequences and use these as a database source file for searching. All
BLAST database source files must be in FASTA format. In order to use
the formatdb option -o T, especially for use with NCBI tool kit retrieval
tools the FASTA defline must follow a specific format.

F) Note on creating an alias file for a GI list.

Formatdb can now produce a BLAST database alias file that specifies a (real)
BLAST database to search as well as a GI list to limit the search. This
is useful if one often searches a subset of a database (e.g., based
on organism or a curated list). The alias file makes the search appear as
if one were searching a real database rather than the subset of one.
The procedure to produce an alias file for searching (protein) nr limiting it to a
list of zebrafish GI's would be:

1.) obtain the list of zebrafish GI's from Entrez or some other source and
keep it in a file called "zebrafish.gi.in".

2.) invoke formatdb to convert the text GI list to the more efficient binary format:

formatdb -F zebrafish.gi.in -B zebrafish.gi

3.) invoke formatdb with the following options:

formatdb -i nr -p T -L zebrafish -F zebrafish.gi -t "My zebrafish database"

This will produce the alias file zebrafish.pal listing the database title, the
real database to be searched, the GI file, and some statistics:

#
# Alias file created Thu Jul 5 15:04:29 2001
#
#
TITLE My zebrafish database
#
DBLIST nr
#
GILIST zebrafish.gi
#
#OIDLIST
#
NSEQ 1836
LENGTH 640724

One can search this by invoking (for example):

blastall -p blastp -d zebrafish -i MYQUERY -o MYOUTPUT

NOTE: One may wish to prepare the alias file in one directory, but move it
to a different production directory that does not contain the real database.
In that case you may use the '-n' option to specify a path to the real
database in the production environment. In the example below the -n option is
used to specify that the nr database can really be found at a relative path
of ../../newest_blast/blast

formatdb -i nr -n ../../newest_blast/blast/nr -p T -L zebrafish -F zebrafish.gi -t "My zebrafish database"

and the alias file will be:

#
# Alias file created Wed Nov 28 13:55:41 2001
#
#
TITLE My zebrafish database
#
DBLIST ../../newest_blast/blast/nr
#
GILIST zebrafish.gi
#
#OIDLIST
#
NSEQ 1836
LENGTH 640724

Notes on Version 4 of the BLAST databases
-----------------------------------------

Version 4 of the BLAST databases address some important
shortcomings of the current (version 4) databases:

1.) Version 3 does not handle ambiguity characters correctly if a
database sequence is longer than about 16 million bases which may
lead to incorrect results. The new version does.

2.) Version 3 only allows one volume of a BLAST database to
contain at most about 4 billion bases. The new databases allows that to
be much larger.

The new databases keep the sequence descriptors in a structured format
(ASN.1) and some new information has been put into those fields. The new
information is:

1.) taxid. This integer specifies the taxonomy of the sequence and will
allow greater flexibility in how taxonomic information is presented in a
future version of BLAST.

2.) link bits. These specify whether LinkOut information about the database
sequence is available and permits the additon of a gif with a link to the relevant page.
in a future version of BLAST.

3.) membership bits. These specify that a given gi in a database also belongs to
a subset database. An example of this relationship is the EST's database. Est
contains all EST's, but also comprises est_human, est_mouse and est_others; with
the new membership bit it will be possible to search any of the subset est databases
with only the main est database and two other small files (an alias file and an "oidlist").
This can reduce the amount of disk-space and memory needed by half in this case.
It is expected that the proper alias file and oidlist for searching such subsets will
be made available on the NCBI FTP site in mid January.

FASTA Defline Format
--------------------
The syntax of FASTA Deflines used by the NCBI BLAST server depends on
the database from which each sequence was obtained. The table below lists
the identifiers for the databases from which the sequences were derived.

Database Name Identifier Syntax

GenBank gb|accession|locus
EMBL Data Library emb|accession|locus
DDBJ, DNA Database of Japan dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT sp|accession|entry name
Brookhaven Protein Data Bank pdb|entry|chain
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier

For example, an identifier might be "gb|M73307|AGMA13GT", where the "gb" tag
indicates that the identifier refers to a GenBank sequence, "M73307" is its
GenBank ACCESSION, and "AGMA13GT" is the GenBank LOCUS.

"gi" identifiers are being assigned by NCBI for all sequences contained
within NCBI's sequence databases. The 'gi' identifier provides a uniform
and stable naming convention whereby a specific sequence is assigned
its unique gi identifier. If a nucleotide or protein sequence changes,
however, a new gi identifier is assigned, even if the accession number
of the record remains unchanged. Thus gi identifiers provide a mechanism
for identifying the exact sequence that was used or retrieved in a
given search.

For searches of the nr protein database where the sequences are derived
from conceptual translations of sequences from the nucleotide databases
the following syntax is used:

gi|gi_identifier

An example would be:

gi|451623 (U04987) env [Simian immunodeficiency..."

where '451623' is the gi identifier and the 'U04987' is the accession
number of the nucleotide sequence from which it was derived.

Users are encouraged to use the '-I' option for Blast output which will
produce a header line with the gi identifier concatenated with the database
identifier of the database from which it was derived, for example, from a
nucleotide database:

gi|176485|gb|M73307|AGMA13GT

And similarly for protein databases:

gi|129295|sp|P01013|OVAX_CHICK

The gnl ('general') identifier allows databases not on the above list to
be identified with the same syntax. An example here is the PID identifier:

gnl|PID|e1632

PID stands for Protein-ID; the "e" (in e1632) indicates that this ID
was issued by EMBL. As mentioned above, use of the "-I" option
produces the NCBI gi (in addition to the PID) which users can also
retrieve on.

The bar ("|") separates different fields as listed in the above table.
In some cases a field is left empty, even though the original
specification called for including this field. To make
these identifiers backwards-compatiable for older parsers
the empty field is denoted by an additional bar ("||").

BLAST Databases without GI's or GenBank accessions
--------------------------------------------------
Some BLAST users wish to format a FASTA file of sequences that do not
contain NCBI ID's such as accessions or GI numbers. This may be the
case if the sequences have not yet been submitted to GenBank or are
proprietary. If the only goal is to perform BLAST searches and format
a standard BLAST report then the simplest solution is to not set the
"-o" option when running formatdb and indices for the identifiers will
not be constructed. If one wishes to produce XML or ASN.1 output or
wants to fetch sequences by ID with fastacmd, it is necessary to
observe a few simple rules when constructing the ID's. These rules are
necessary to ensure that the ID's can be reliably parsed to make the ID
indices.

1.) ID's of type "local" or "general" should be used. This means that
the ID's will have the syntax "lcl|IDENTIFIER" (for "local") or
"gnl|DATABASE|IDENTIFIER" (for "general"). The tokens DATABASE and
IDENTIFIER should be assigned by the user here. The local ID has only
one user provided token, the general ID requires two. The fields are
separated by vertical bars ("|")..

2.) Letters, numbers, underscores ("_"), dashes, and periods may be
used. Uppercase and lowercase letters are treated as being distinct.
No spaces are allowed in the ID, this indicates the end of the ID.

3.) All ID's should be unique, if the entire ID is examined. As an
example consider the following four ID's:

All of these ID's are considered unique. The first two might be
sequences one and two of a collection of Human sequences; the fourth
might be the first sequence in a collection of mouse sequences; the
fourth is simply identified as the first sequence.

ID's must fit into the framework described above to ensure that they
can be reliably parsed and indices built for them. This means that it
is not possible for users to invent new ID formats on the fly.
Examples of illegal ID's would be:

H.sapiens|seq1
gnl|H.sapiens|seq1|A

The first identifier is missing a database tag (e.g., no "lcl"), the second
identifier has an extra field since vertical bars separate fields. Illegal
ID's will not be processed by formatdb if the "-o" option is used.

F. General troubleshooting tips.

The Latest Version: Make sure you are using the latest version of the
formatdb executable. Earlier versions of formatdb may not recognize
changes in the ASN.1 or FASTA definition line format of current BLAST
databases or other sources of NCBI sequences.

G. Troubleshooting "SeqIdParse Failure" errors

The most frequent cause of SeqIdParse Failure errors come from the
syntax of the FASTA definition lines in the source database file. Many
third parties do not follow the syntax in section F. If you are
getting a SeqIdParse error this can often be eliminated by formatting
the database with the -o option set to FALSE (e.g. -o F). The -o option
is really not important for BLAST searching unless you are going to use
the results to parse out the identifiers for searching Entrez and
downloading the sequences. If you need to use the -o T option then your
best option is to examine the definition lines of the database sequences
and attempt to make them conform the FASTA syntax.

H. Troubleshooting "FileOpen" errors.

This is caused when the formatdb program can not find the /data
subdirectory. When you download and extract the Standalone BLAST
executables, the formatdb program is located in the same directory as
the /data subdirectory. If either if these move, formatdb will not
function without a .ncbirc file telling it where the /data subdirectory
resides. Create a text file in the same directory as formatdb that
contains the following lines:

[NCBI]
Data="path/data/"

Where "path/data/" is the path to the location of the Standalone BLAST
"data" subdirectory. For Example:

Data=/root/blast/data

For PC's this would be

[NCBI]
Data="C:\path\data\"

Where "C:path\data\" is the path to the location of the Standalone
BLAST "data" subdirectory. For example:

Data=C:\blast\data

For Macintosh this would be a simpletext file called "ncbi.cnf", placed in
System folder, that contains:

[BLAST]
BLASTDB=root:blast:data

Where "root:blast:data" is the path to the location of the Standalone
BLAST "data" subdirectory. For example on the machine names "LabMac":

BLASTDB=LabMac:blast:data

Appendix 1: The Files Produced by Formatdb
------------------------------------------
Using formatdb without the "-o T" indexing option results in three
BLAST database files (.nhr, .nin, ,nsq). Using the "-o T" option will result in
additional files.
If gi's are present in the FASTA definition lines of the source file, there will
be four additional files created (.nsd, nsi, nni, nnd). These are ISAM indices for
mapping a sequence identifier to a particular sequence in the BLAST database If
gi's are not use there will be only two additional files created (.nsd, .nsi).
These files are listed below for both an example nucleotide and a protein sequence
database. The actual sequence data is stored in the files with extension "nsq" or
"psq". The compression ratio for these files is about 4:1 for nucleotides and 1:1
for protein sequence source files.

Extension Content Format
---------------------------------------------
Nucleotide database formatted without "-o T"

nhr deflines binary

nin ISAM binary

nsq ISAM binary

Nucleotide database formatted with "-o T" add these:

nsd parsed binary
deflines

nsi gis binary

nni ISAM binary

nnd ISAM binary

The formatdb index files involving deflines are small relative to the
source database due to entries such as the one below in which the
defline is much shorter than the sequence.

>gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete genome
GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGCT
TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATTT
GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAAC
TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGACA
GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACATG
AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAGC
CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATCC
CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCTC
GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTTA
....16398 bp total

Extension Content Format
------------------------------------------
Protein database formatted without "-o T

phr deflines binary

pin ISAM binary

psq ISAM binary

Protein database formatted with "-o T" add these:

pnd ISAM binary

pni ISAM binary

psd parsed binary

psi gis binary

The formatdb index files involving deflines are large relative to the
source database due to entries such as the one below in which the
defline is much longer than the sequence.

>gi|229659|pdb|1AAP|A Chain A, Protease Inhibitor Domain Of Alzheimer's
Amyloid Beta-Protein Precursor (APPI)gi|229660|pdb|1AAP|B Chain B,
Protease Inhibitor Domain Of Alzheimer's Amyloid Beta-Protein Precursor
(APPI)
VREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSA

DISCLAIMER: The internal structure of the BLAST databases is subject
to change with little or no notice. The readdb API should be
used to extract data from the BLAST databases. Readdb is part
of the the NCBI toolkit (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/),
readdb.h contains a list of supported function calls.

Last updated April 02 2001