July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
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20 Tips to Improve Your BLAST Searches
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8.8 Mask Repeats in Genomic DNA
As mentioned in Chapter 2, genomes may be full of repetitive elements and low-
complexity sequence. They can be very problematic in BLAST searches, and if not
masked prior to a BLAST search, will waste computer time and inflate BLAST
reports with meaningless, redundant information (Figure 8-4).
8.9 Segment Large Genomic Sequences
Nucleotide sequences can be very, very long. For example, the shortest human chro-
mosome, number 22, is over 47 million bp. BLAST wasn’t designed for large
sequences and runs poorly in such an environment. You can easily run out of mem-
ory with chromosome-sized sequences. Even if you have a computer with sufficient
memory, searching large sequences is inefficient because the procedure for assessing
combined statistical significance scales quadratically with the number of alignments.
Figure 8-3. Complexity filters (a) hard-masking and (b) soft-masking
Figure 8-4. BLASTX search with (a) repeats intact and (b) repeats masked (the alignments were
removed from the display)
a
b
Score = 70.1 bits (170), Expect = 5e-12
Identities = 35/79 (44%), Positives = 45/79 (56%)
Query: 1 MAVTQXXXXXXXXXXXXXXXXXXPSEITPEKSFVDDLDIDSLSMVEIAVQTEDKYGVKIP 60
MA TQ ++ +KSF DDLD+DSLSMVE+ V E+++ VKIP
Sbjct: 1 MAATQEEIVAGLADIVNEIAGIPVEDVQLDKSFTDDLDVDSLSMVEVVVAAEERFDVKIP ...
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