BLAST

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xdformat Parameters

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wordmask=[method]

Default: Off

Filters the query sequence for seeding only. Low-complexity region in the query sequence

isn’t used in the initial word search but is available for alignment during the extension

stage; called soft masking.

See also

filter, lcfilter, lcmask, echofilter, maskextra

W=[integer]

Default: 11 blastn, 3 others

Sets the word size for seeding alignments.

See also

T, hitdist, wink

X=[integer]

Default: Variable; depends on scoring parameters

Controls the alignment extension cutoff for ungapped alignments.

See also

gapX

Y=[number]

Default: Variable; depends on scoring parameters

Sets the size of the query sequence.

See also

Z

Z=[number]

Default: Variable; depends on scoring parameters

Sets the size of the database in letters (restest is assumed), but Z may also be used to mean

the number of sequences if

seqtest is set.

See also

Y, seqtest, restest

xdformat Parameters

xdformat formats BLAST databases from FASTA files. It also reports descriptive

information about the database and dumps the entire content to FASTA format.

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Chapter 14: WU-BLAST Reference

Here are some examples:

xdformat -n files

xdformat -p files

zcat fasta.*.gz | xdformat -o my_db -n -- -

xdformat -n -i database

xdformat -n -r datatbase > fasta_file

-A [0..2]

Default: 2

When indexing accession.version identifiers, you have three indexing options:

0 Accession only; version isn’t stored

1 Stored as accession.version

2 Stored as both accession only and accession.version

-a [database]

Appends sequences to the named database. If the database is indexed, the appended

sequences will also be indexed.

-c [character]

Default: Off

If an invalid letter is encountered, xdformat terminates and reports an error message. If this

occurs, check the sequence file for errors. After checking, you may either skip illegal char-

acters with

-k or change them to a legal character with -c. The typical operation for

nucleotides is to set

-c N, and for proteins -c X.

See also

-k

-D [integer]

Default: Unlimited

Sets the maximum length for definition lines.

-d [string]

Default: None

Sets a user-defined release date for the database. The date may have 63 characters at most.

See also

-v

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xdformat Parameters

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-e [file]

Default: stderr

Appends information and errors to the named file.

-G

Default: Off

Prefaces each sequence with the database record number in the format of gnl|xdf|#.

-i

Default: Off

Reports descriptive information about a BLAST database. This is useful for determining

when a database was created, how many sequences it contains, and if it is indexed.

-K [integer]

Default: Unlimited

Sets the maximum number of identifiers with Control-A separators. This is useful for trim-

ming highly redundant sequences created with nrdb or another redundancy purifier that

uses Control-A separators.

-k

Default: Off

If an invalid letter is encountered, xdformat terminates. If this occurs, you can either skip

illegal characters with

-k or change them to a legal letter with -c. Check the errors to

ensure the input file is formatted properly.

See also

-c

-L [number]

Default: 100000000 (100 million letters)

Sets the maximum sequence length. For optimal performance, break up large sequences

into smaller fragments no larger than 1 million letters.

-l [number]

Default: 0

Sets the minimum sequence length.

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Chapter 14: WU-BLAST Reference

-M [number]

Default: 96m

Sets the cache size for indexing. For faster indexing, the size may be increased (for example,

-M 512m).

-O [4..8]

Default: 4

Sets the number of bytes of precision. The default value allows databases of up to 4 billion

amino acids or 16 billion nucleotides. If you expect a database to contain more than this

limit, increasing precision by one level multiplies the limit by 256. Setting

-O is necessary

only if you append to the database because the precision automatically increases appropri-

ately when databases are created.

-P [integer]

Default: 60

This option applies only when dumping the entire content of a database with -r. -P

controls the length of the sequence lines; -P 0 puts the whole sequence on one line.

See also

-r

-q [0..3]

Default: 0

Certain files may contain numerous nonfatal errors in their identifier format. -q quiets

these errors.

0 No silencing

1 Silences field1 errors

2 Silences field 2 errors

3 Silences all fields

-r

Default: Off

Reports (dumps) the entire database content to stdout in FASTA format.

-T [string]

Default: Off

This option lets you restrict indexing of identifiers to a particular database name or tag.

The [string] has two parts: part 1 is the name of the database (e.g.,

gb for GenBank or emb

for EMBL—see Chapter 10), and part 2 is either blank or a number.