Example 1: E. coli tRNA homologues in archaean genomes

Query: E. coli K12 tRNA (valV, selC, asnV, leuT, argZ from EMBL entry U00096)
Database: EMBL entries AE017261, AE004437, AE000782, AE009441, AE006641

Results

BLASTN (both) | FASTA | Nhunt

The coordinates of the obtained hits were compared with the coordinates of annotated archaean tRNA.
Each point corresponds to one output alignment.
Values on the X and Y axes are total lengths of, respectively, "wrong" and "right" fragments of the alignments with scores greater than the score of the given alignment.

Run time (3.0 GHz dual-core processor)

BLASTN (optimal): 3.5 s
BLASTN (default): 0.8 s
FASTA: 13 s
Nhunt: 7 s

Inference

The program Nhunt surpass all other tested programs in sensitivity.
Note that the change of BLASTN options leads to a dramatic increase of sensitivity.

Example 2: E. coli rRNA homologues in archaean genomes

Query: Fragment of the E. coli K12 16S rRNA (gene rrsH from EMBL entry U00096)
Database: EMBL entries AE017261, AE004437, AE000782, AE009441, AE006641

Results

BLASTN (optimal) | BLASTN (default) | discontiguous MEGABLAST | FASTA | Nhunt

Run time (3.0 GHz dual-core processor)

BLASTN (optimal): 2.9 s
BLASTN (default): 0.14 s
Discontiguous MEGABLAST: 0.19 s
FASTA: 7 s
Nhunt: 3.7 s

Inference

BLASTN with default parameters actually cannot find any significant homologues.

Example 3: E. coli miscRNA homologues in Bacillus genomes

Query: E. coli 55989 miscRNA (gene C0067 from EMBL entry CU928145)
Database: EMBL entries CP001176,

Results

BLASTN (optimal) | BLASTN (default) | discontiguous MEGABLAST | FASTA |
Nhunt-1 (no adjustment, '-a 0') |
Nhunt-2 (adjustment for local alignment only, '-a 1') |
Nhunt-3 (adjustment both for local alignment and output scores calculating, '-a 3')

Run time (3.0 GHz dual-core processor)

BLASTN (optimal): 2.2 s
BLASTN (default): 0.16 s
Discontiguous MEGABLAST: 0.19 s
FASTA: 4.3 s
Nhunt-1: 3.7 s
Nhunt-2: 1.6 s
Nhunt-3: 1.7 s

Inference

BLASTN with default parameters actually cann't find any significant homologues.
Nhunt with adjustment switched on dramatically decrease the significance of found alignments.
Discontiguous MEGABLAST can not find any alignment at all.

For more integrate impression try it yourself!

Copyright 2010-2011 Yury Pekov