question about BLAT score

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Tracey Flint Zacharov

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Sep 11, 2013, 3:02:01 AM9/11/13

to gen...@soe.ucsc.edu

Hi!

Could you explain exactly how the “score” is calculated in the BLAT results table? I understood it was supposed to be number of matches but that is not the case as in the table below 82 bases match and the score is 68, so there must be some penalty for gaps or something.

Example:

BLAT Search Results

   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN

---------------------------------------------------------------------------------------------------

browser details YourSeq           68    22   279   346  88.0%    18   +   40079373  40079639    267

Details:

Alignment of YourSeq and chr18:40079373-40079639

Click on links in the frame to the left to navigate through the alignment. Matching bases in cDNA and genomic sequences are colored blue and capitalized. Light blue bases mark the boundaries of gaps in either sequence (often splice sites).

cDNA YourSeq

accggtgcta gcatggtaca tTTGTCAAAA CTAAGAAAaG tACctTgGct  50

CccTACTGTT AACTAAAgtc ctgacttttg gggatttccc cagctttctc  100

gtgtcctttt tctgtcccag gatcctgtcc aggattactg tattgcgttt  150

agtcttcatg tgtcctttga tctctgatct gtgacggttt ctgaatcttt  200

ttttgttttt catgaCCTTG ATAGTTTTGA GGAGTACTGa taggtatttt  250

gtggattgTC CCTCAGTTTG GGTTTGTCTc atggtttctt ctgattagat  300

tggagataca gatttttttt tttttttttt tntttttttn ggcccc

Genomic chr18 :

tgtcttttta agagtaactt gttatgggag ccctaggaaa ccaattcaac  40079322

tcctcaccca acttcctcta atgttcatgt cttaaattgc cattttatag  40079372

TTGTCAAAAC TAAGAAAtGa ACacTaGtaC atTACTGTTA ACTAAActgt  40079422

agtccttatt tggatttcct tacttttaac actaacatcc ttttttcctg  40079472

gggaacaatc taggatactt cactgcattt agctatcatg tctccttagt  40079522

catccctgag atgtgacagt ttctcagcat tttttttttt ttattagtag  40079572

CCTTGacATA GTTTTGAGGA GTACTGctca gttgttttat agaataTCCC  40079622

TCAGTTTGGG TTTGTCTtga ccaaagtcat ggactttggg gaagaatact  40079672

aatgttttat ttatctttat atactcattg ctaaccacat actagctaat  40079722

tttcaatacc cagttat

Side by Side Alignment

00000022 ttgtcaaaactaagaaaagtaccttggctccctactgttaactaaa 00000067

>>>>>>>> ||||||||||||||||| | ||  | |  |  |||||||||||||| >>>>>>>>

40079373 ttgtcaaaactaagaaatgaacactagtacattactgttaactaaa 40079418

00000216 ccttg..atagttttgaggagtactg 00000239

>>>>>>>> |||||  ||||||||||||||||||| >>>>>>>>

40079573 ccttgacatagttttgaggagtactg 40079598

00000259 tccctcagtttgggtttgtct 00000279

>>>>>>>> ||||||||||||||||||||| >>>>>>>>

40079619 tccctcagtttgggtttgtct 40079639

Thanks for your help

Tracey

Pauline Fujita

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Sep 11, 2013, 5:20:11 PM9/11/13

to Tracey Flint Zacharov, gen...@soe.ucsc.edu

Hello Tracey,

You can find a description of the BLAT methods and parameters in these
help docs:

http://genome.ucsc.edu/FAQ/FAQblat.html
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign
http://genome.ucsc.edu/goldenPath/help/blatSpec.html

In particular this section of the FAQ explains the score calculations:

http://genome.ucsc.edu/FAQ/FAQblat.html#blat4

Hopefully this gets you the answers you are looking for. If you have
further questions please feel free to contact the mailing list again
at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu