170 7 Sequence Similarity Searching Tools
search. The disadvantage of PHI-BLAST is that it is designed to combine
pattern search with the search for statistically significant sequence similarity,
rather than to maximize search sensitivity.
Note that PHI-BLAST uses the same website as PSI-BLAST.
WU-BLAST2 http://www.ebi.ac.uk/blast2
This is a new version of WU-BLAST that uses sum statistics for gapped align-
ments (Altschul and Gish 1996).
MegaBLAST http://www.ncbi.nlm.nih.gov/blast/mmtrace.shtml
This algorithm introduces a “greedy” alignment algorithm that can perform
much faster than the traditional dynamic programming algorithm for se-
quence alignment (Zhang et al. 2000). See alsowww.ncbi.nlm.nih.gov/
blast/tracemb.shtml.
RPS-BLAST
genopole.toulouse.inra.fr/blast/rpsblast.html
Reverse PSI-BLAST searches a query sequence against a database of pro-
files (Marchler-Bauer et al. 2002). This is the opposite of PSI-BLAST, which
searches a profile against a database of sequences. RPS-BLAST uses a BLAST-
like algorithm, finding single- or double-word hits and then performing an
ungapped extension on these candidate matches. If a sufficiently high-scoring
ungapped alignment is produced, a gapped extension is performed and the
gapped alignments with sufficiently low expectation value are reported. RPS-
BLAST uses a BLAST database, but also has some other files that contain
a precomputed lookup table for the profiles to allow the search to proceed
faster. RPS-BLAST is available at both the NCBI web server and the BLOCKS
web server.
MPBLAST blast.wustl.edu
This is a program that increases the throughput of batchblastnsearches by
multiplexing (concatenating) query sequences to reduce the number of ac-
tual database searches performed (Korf and Gish 2000). Throughput was ob-
served to increase in inverse proportion to the component sequence length.
In other words, shorter component queries benefit more from MPBLAST
than longer component queries. For component DNA queries of length 500,
an order of magnitude speedup has been observed.
PathBLAST
http://www.pathblast.org/bioc/pathblast/blastpathway.jsp
This is a network alignment and search tool for comparing protein inter-
action networks across species to identify protein pathways and complexes