BLAST

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Chapter 8: 20 Tips to Improve Your BLAST Searches

Figure 8-7 demonstrates another feature of gapped alignment: alignments may

extend far beyond the end of an exon because gapped extension is generally less spe-

cific. This is especially annoying in genomes with short introns in which gapped

alignments can extend between nonadjacent exons and obscure intervening introns

and exons. To reduce these lengthy extensions, decrease X, increase the gap exten-

sion cost, select a more stringent scoring matrix, or use ungapped alignment.

8.15 Look for Gaps in Coverage as a Sign

of Missed Exons

The seeding parameters and alignment thresholds may prevent short or highly diver-

gent exons from appearing in BLAST reports. Figure 8-8a shows an alignment

between a genomic query and an EST. Most alignments overlap by a few bp, except

for the 2 at the 5´ end (left side). Gaps and overlaps in coverage are easier to see by

using the reciprocal search shown in Figure 8-8b. To find the missing 7-bp exon in

Figure 8-8c, use bl2seq (see Chapter 13) with the following command line:

bl2seq -i est -I 21,29 -j genomic -J 76047,76744 -pblastn -W 7

The -I and -J parameters let you select a specific region of each sequence. What

you’ve done is a BLASTN search between the missing part of the EST and the region

between ...