Download BLAST and Regular Expression Searches

BLAST & Regular Expression
Searches Functionality
Susie Stephens
Life Sciences Product Manager
Oracle Corporation
2#
BLAST in the Database
• Implemented using a table function interface
• BLAST search functions can be placed in
SQL queries
• Different functions for match and align
• SQL queries can be used to pre-filter
database of sequences and post-process the
search results
• Combination of SQL queries and BLAST is
very powerful and flexible
3#
Stand-alone BLAST Server
• Sub select the sequence
database
• Export the sequences
• Create BLAST dataset
• Run BLAST search
Export
FormatDB
Sequence
DB
• Import search result into
database
Import
exportFile
BLAST DB
Search
Result
BLAST
Server
• Write SQL queries for further
analysis
4#
Core Functionality of BLAST
• Implemented an NCBI BLAST 2.0-like version
of BLAST
• Implemented the 5 core variants
– BLASTN: Nucleotide sequence vs. nucleotide db
– BLASTP: Protein sequence vs. protein db
– TBLAST: Searches involving translations
• BLASTX: translated nucleotide sequence vs. protein db
• TBLASTN: protein sequence vs. translated nucleotide db
• TBLASTX: translated nucleotide sequence vs. translated
nucleotide db
5#
BLAST Interface
select
from
t.seq_id, t.score, t.expect
Table(BLASTN_MATCH(
seq_id, score, expect
‘ATCGAGTACGTACAT’,
cursor (select seq_id, sequence
from GENE_DB
BLASTN_MATCH
where organism = ‘human’),
5, /* expect_value */
12)) t /* word_size */
query_sequence, parameters
organism = ‘human’

GENE_DB
6#
BLAST GUI
7#
Regular Expression Searches
• Powerful method of describing simple and
complex patterns for searching and manipulating
• Multilingual regular expression support for SQL
and PL/SQL string types
• Follows POSIX style Regexp syntax
• Support standard Regexp operators
• Compatible with popular Regexp
implementations like GNU, Perl, Awk
8#
Features
•
•
•
•
•
•
•
•
•
•
Quantifiers
Grouping
Back References
Character Classes
Anchors
Backtracking
Greediness
LOB Support
Match Options
Locale Sensitive
‘.’ any one character
‘+’ one or more
‘*’ zero or more
‘?’ zero or one
‘{m,n}’ between m and n
‘|’ infix or
‘()’ group
‘[ .. ]’ any in the list
‘[^ .. ]’ any not in the list
‘\n’ reference nth group
‘^$’ line/string anchor
‘[:c:]’ classes
9#