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NCBI (GenBank) Sequence Scanner

Description:

With a GenBank accession ID, locate a subsequence within the associated sequence at a specific relative distance from the start of the record.

Rationale:

Many publications describe sequences in a genome that are regulatory however, these sequences may have moved between genomic builds or may not be easy to locate within the upstream sequence. This script takes an GenBank accession ID and interrogates an associated sequence for matches to small input sequences. For instance, if a publication reports the sequence "ATATATAT" as regulatory , this script will find all matches within a defined sequence region in a GenBank record and report them.

Script:

Enter NCBI Accession ID:
HELP: Find NCBI Accession IDs
EXAMPLE:
L11910 (Human)
Relative Start:
EXAMPLE: 1 (from record start)
Relative End:
EXAMPLE: 1000 (from record start)
Strand:
Scan Sequence 1:
EXAMPLE: CGCGCGCG
Scan Sequence 2 (optional):
EXAMPLE: ATATATAT
 

Questions or comments to oreganno@bcgsc.ca. (Archived here)