8.1 Command-Line Options

Table 8-1 summarizes the BLAT options.

Table 8-1. BLAT options





Output dot every N sequences to show the program's progress.



Make overused tile file.



Mask out repeats. Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Types are:

lower = Mask out lowercased sequence.

upper = Mask out uppercased sequence.

out = Mask according to database.out RepeatMasker .out file.

file.out = Mask database according to RepeatMasker file.out.



Sets the size of maximum gap between tiles in a clump. Usually set from 0 to 3.

Only relevant for minMatch > 1.



Sets minimum sequence identity (in percent).

90 (nucleotide)

25 (protein)

25 (translated)


Sets the number of tile matches. Usually set from 2 to 4.

2 (nucleotide)

1 (protein)


Sets minimum score. This is twice the matches minus the mismatches minus some sort of gap penalty.



Minimum percent divergence of repeats to allow them to be unmasked. Only relevant for masking using RepeatMasker .out files.



Suppress .psl header (so it's just a tab-separated file).



Don't trim trailing poly-A.



If set to 1, this allows one mismatch in tile and still triggers an alignment.



Use overused tile file N.ooc. N should correspond to the tileSize.



Controls output file format. Type is one of:

psl = Tab-separated format without actual sequence.

pslx = Tab-separated format with sequence.

axt = blastz-associated axt format.

maf = multiz-associated maf format.

wublast = similar to wublast format.

blast = similar to NCBI blast format.



Synonymous to -d=prot -q=prot.



Mask out repeats in query sequence. Similar to -mask, but for query rather than target sequences.



Query type. Type is one of:

dna = DNA sequence.

rna = RNA sequence.

prot = protein sequence.

dnax = DNA sequence translated in six frames to protein.

rnax = DNA sequence translated in three frames to protein.



Sets the number of repetitions of a tile allowed before it is marked as overused. Typically this is:

256 for tileSize 12.

1024 for tile size 11.

4096 for tile size 10.

Typically comes into play only with makeOoc.



Database type. Type is one of:

dna = DNA sequence.

prot = protein sequence.

dnax = DNA sequence translated in six frames to protein.



Sets the size of match that triggers an alignment. Usually between 8 and 12.

11 (DNA)

5 (protein)


Removes poly-A tail from qSize and alignments in psl output.



Trims leading poly-T.

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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