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

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| Query | Target | Total | |type | Strands | Frames | Strands | Frames | Searches |

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| dna | 2 | 1 | 1 | 1 | 2 | | prot | 1 | 1 | 2 | 3 | 6 | | rnax | 1 | 3 | 2 | 3 | 18 | | dnax | 2 | 3 | 2 | 3 | 36 |

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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.

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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