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172 7 Sequence Similarity Searching Tools

genome likely to be homologous to the query sequence. It performs an align-

ment between homologous regions. It stitches together these aligned regions

(often exons) into larger alignments (typically genes). Finally, BLAT revisits

small internal exons possibly missed at the first stage and adjusts large gap

boundaries that have canonical splice sites where feasible.

Figure 7.4 BLAT input window.

We illustrate the use of BLAT with a search of a 718-bp DNA sequence

(GenBank accession number AF200505.1) encoding exon 4 of thePongo pyg-

maeusApoE gene using the BLAT server atsnp.ims.u-tokyo.ac.jp/

map/cgi-bin/Blat/blat_genome.cgi. Figure 7.4 shows the input win-

dow, and figure 7.5 shows the output window, where the human ApoE gene

was found to be similar to the query DNA sequence.

Summary

Many variations and enhancements of BLAST have been introduced:

1. Performance improvements in special cases or in general:
   
   
   • bl2seq: 2 sequence comparison;