Loaded into memory for a detailed alignment. The index is used to find areas of probable homology, which are then The genome itself is not kept in memory, allowingīLAT to deliver high performance on a reasonably priced Linux box. RAM can be further reduced to less than 1 GB by increasing step size to 11. The index takes up aboutĢ gigabytes of RAM. The index consists of all overlapping 11-mers stepping by 5 except for DNA BLAT works by keeping an index of the entire genome In practice DNA BLAT works well on primates, and proteinīLAT is not BLAST. It will findīLAT on proteins finds sequences of 80% and greater similarity of length 20 aminoĪcids or more. It may miss more divergent or shorter sequence alignments. Quickly find sequences of 95% and greater similarity of length 25 bases or See our BLAT FAQ for more.įor locating PCR primers, use In-Silico PCR for best results instead of BLAT. This checkbox can be useful with short queries and with the tiny genomes of microorganisms.įor programmatic access, BLAT supports URL queries which return in JSON format. For example, with a human dna search, 20 is minimum matches required, based on the genome size, to filter out lower-quality results. The All Results checkbox disables minimum matches filtering so all results are seen. See our BLAT All FAQ for more information. Search all is only available for default assemblies and attached hubs with dedicated BLAT servers.The new dynamic BLAT servers are not supported, and they are noted as skipped in the output. The Search all checkbox allows you to search all genomes at the same time. Submissions is 50,000 bases or 25,000 letters.Ī valid example is GTCCTCGGAACCAGGACCTCGGCGTGGCCTAGCG (human SOD1). Up to 25 sequencesĬan be submitted at the same time. Sequence of 10000 or fewer letters will be processed. Only DNA sequences of 25,000 or fewer bases and protein or translated Rather than pasting a sequence, you can choose to upload a text file containing the sequence. If separated by lines starting with '>' followed by the sequence name. Paste in a query sequence to find its location in the BLAT Search Genome Genome: Search all genomes
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