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SesbainaOmics

Multiple-Omics database of Sesbania Species

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BLAT Search

convert BLAT Search

BLAT can find a query sequence's location in a reference genome. It employs UCSC-BLAT to finish this task.
Paste in a query sequence or choose to upload a text file containing the sequence. Multiple sequences may be searched if separated by lines starting with '>' followed by the sequence name.

Note: Only DNA sequences of 25,000 or fewer bases and protein or translated sequence of 10000 or fewer letters will be processed.
Up to 25 sequences can be submitted at the same time. The total limit for multiple sequence submissions is 50,000 bases or 25,000 letters.

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About BLAT

Parameters:

Query type. Type is one of:
     DNA - DNA sequence
     RNA - RNA sequence
     protein - protein sequence
     translated DNA - DNA sequence translated in six frames to protein
     translated RNA - DNA sequence translated in three frames to protein

BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein BLAT on land vertebrates.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250

More information about BLAT can be found hear - UCSC-BLAT .