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OFRG
Sequence Retrieval Tool of OFRG
rDNA Sequence Database Construction

Instruction:
You can skip this step by using default data files: 16SbacteriarRNA or 18SFungirRNA in the next step. The data file can be downloaded from NCBI or from other resources, as long as it is in FASTA format. The name should contain no space. You may ignore the content in "Search" dropdownlist once you specified your file for upload.

Upload your data file

INPUT
Upload sequence file:

In this step: The file will be searched for the sequences that contain both the forward and reverse primers. Please submit the reverse primer in reverse complement format. The resulting sequences will be cut at the primer sites, and then used to form the pattern file in the next step. Degenerate sequences are removed in this step.
PARAMETERS
Search Forward Primer Reverse Primer
Minimum length Maximum length Mismatches

In this step: A homology search is performed to retrieve the seqeuences that are not in the pattern data file but are homologous to the sequences in the pattern data file by using BLAST. Please specify a name (No Space Allowed) under "rDNA Database" for your result to display.
HOMOLOGY SEARCH PARAMETERS
rDNA Database
Symbol Comparison Score Table Open Gap Penalty & Extend Gap Penalty BLAST E_Value
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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013