BLAT-Strands-And-Frames

hgBlat

Most people first meet BLAT though hgBlat on the UCSC Genome Browser. It talks to the gfServer, picking either the dna server or the translated server which are defined in the blatServers table.

BLAT

Strands and Frames and Searches

Type	QStrands	QFrames	TStrands	TFrames	Searches
dna	2	1	1	1	2
prot	1	1	2	3	6
rnax	1	3	2	3	18
dnax	2	3	2	3	36

For blat untranslated target index, it has only + strand indexed in 1 frame.

For blat translated target index, it has both + and - strands indexed in 3 frames.

For dna and dnax, it repeats the search after reverse-complementing the query.

For prot, it only has to deal with the frames and strands of the target. The query side is simple.

For rnax, it converts the query to rna in 3 frames, searching target 6 frames each time.

For dnax, it does rnax, then reverse-complements the query, then does rnax again.

Query Types

Type	Query Type
dna	DNA
prot	Protein
rnax	Translated RNA
dnax	Translated DNA
?	BLAT's Guess

For BLAT's Guess, it will only guess dna or protein. It will never guess rnax or dnax. Also it will only look at the first sequence submitted, and treat all the rest of the sequences submitted like that first one.

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Strand Usage

q = query (what you are searching for)
t = target (usually a genome, what you are searching in)

Strand Notation

PSL	Actual DNA Strand	Query Types	Describes	Equivalent
+	+	dna	qStrand	++
-	-	dna	qStrand	-+
++	+	prot,rnax,dnax	qStrand tStrand
+-	-	prot,rnax,dnax	qStrand tStrand
-+	-	dnax	qStrand tStrand
--	+	dnax	qStrand tStrand