the result from BLAT
Jay Yuan
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- browser details YourSeq 76 1 76 76 100.0% Un_gl000220 + 109835 109910 76 browser details YourSeq 76 1 76 76 100.0% Un_gl000220 + 153807 153882 76 browser details YourSeq 68 1 75 76 91.8% 16 + 33963256 33963328 73 browser details YourSeq 64 1 75 76 90.3% Un_gl000229 + 18929 19001 73 browser details YourSeq 63 1 76 76 90.2% 2 - 133012948 133013021 74 browser details YourSeq 63 1 76 76 89.1% Y + 10035605 10035678 74 browser details YourSeq 22 40 61 76 100.0% 14 - 32543222 32543243 22
yuan
Chris Villarreal
Dear Yuan,
Thank you for your question about BLAT. This question can be answered in detail by accessing the "Using BLAT to Find Sequence Similarity in Closely Related Genomes" paper here,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4101998/, and looking under the "Percent identity calculation" section. Here is an excerpt, "BLAT also provides a percent identity score, p, to indicate differences between sequences preventing a perfect match of 100%. The differences include mismatches and gaps. The score also includes a term for large inserts: for example, when aligning a transcript to the genome, inserts for introns would be necessary."
Here is a link to the Kent BLAT paper, "BLAT--the BLAST-like alignment tool", https://www.ncbi.nlm.nih.gov/pubmed/11932250. I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
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