Download Blast and Pathway Tools

Blast and Pathway Tools
What is BLAST?
Basic Local Alignment Search Tool
- BLAST is a method for rapid searching of nucleotide or
protein databases.
-It is essentially a rapid sequence alignment tool.
- BLAST algorithms detect local alignments.
What are you looking for by running a blast query?
Possibilities:
Where should you go looking for
this? (i.e. what is your target
database?).
What kind of BLAST
search should you run?
Are you looking for an
exact match of your
sequence in the
database?
Nucleic acid databases such as
genome, EST, or ORF databases.
blastn
Protein database. Your input should
be amino acid or protein coding
nucleic acid.
blastp for amino acid
queries; blastx for translated
nucleic acid queries. Use
tblastn or tblastx for
comparisons of an amino
acid or translated nucleic
acid query versus a
translated nucleic acid
database.
Are you looking for
homologs/orthologs of
your sequence in the
database?
Special Cases
Defaults
Short Query
Large Sequence
Family
Ungapped
BLAST
Filter
on
off
on
on
Scoring Matrix
BLOSUM62
PAM30 for 35
and under
BLOSUM62
BLOSUM62
E value
0.05
1000 or more
(You expect
more hits)
default
default
Alignments
50
50
2000
50
Blast output
(live web-based demo)
Metabolic Pathways
KEGG: Kanehisa, M. et al. Nucl. Acids Res. 2008 36:D480-D484; doi:10.1093/nar/gkm882
MetaCyc: Caspi, R. et al. Nucl. Acids Res. 2008 36:D623-D631; doi:10.1093/nar/gkm900
KEGG: Kyoto
Encyclopedia of
Genes and
Genomes
The new KEGG
metabolism map
created as an
SVG file
Kanehisa, M. et al. Nucl. Acids Res. 2008 36:D480-D484; doi:10.1093/nar/gkm882
An example of a pathway in MetaCyc
Caspi, R. et al. Nucl. Acids Res. 2008 36:D623-D631; doi:10.1093/nar/gkm900
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