BLAT Search Genome

URL:

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

What you can do:

Quickly find sequences of 95% and greater similarity of length 40 bases or more for DNA or 80% and greater similarity of length 20 amino acids or more for protein in a genome.

Highlights:

As a sequence alignment tool, BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
It uses the index to find regions in the genome likely to be homologous to the query sequence.
It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes).
BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible.
Users can find the locations of their query sequences from nearly 30 model organism genomes.
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.
In practice DNA BLAT works well on primates, and protein blat on land vertebrates.

Keywords:

DNA sequence search
genomic sequence mapping tool
sequence alignment tool
protein sequence search
protein sequence alignment
genome mapping
EST sequence mapping

Literature & Tutorials:

PubMed Link: BLAT--the BLAST-like alignment tool