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Remapped CDF Web Server Software

How to use Web Server

The figure shows the screenshot of the web server.



There are four steps to finish the submission task.

Step 1: Select FASTA format probe sequence input file and Affymetrix CDF file

The first file is the probe sequence file in FASTA format. The header of the FASTA format is in the following format:

  • >OPID|X|Y
where OPID is the original probe set identifier, X and Y are coordinates on the chip.
The second file is the Affymetrix CDF file which can be downloaded from < a href="http://www.affymetrix.com">the Affymetrix website. The file provides necessary control probe sets which will be used by microarray data analysis software.


Step 2: Select parameters

There are five parameters needed to be set.
Parameter Description Allowed values
Organism Identify the organism of the chip Human, Mouse, and Rat etc
Probe grouping Criteria Specify the probe grouping criteria transcript-consistent (grouping according to transcript) or gene-consistent (grouping according to gene)
Use sequences from Specify the target sequence databases Our complete coding sequences or RefSeq
Accept only probe sets that are consistent or unique Specify whether to keep or to ignore ambiguous probe sets Consistent (keep ambiguous probe sets) or Unique (ignore ambiguous probe sets)
Minimum number of probes in remapped probe set Specify the minimum number of probes in remapped probe set The value needs to be a positive integer
Maximum number of mismatches allowed during mapping Specify the maximum number of mismatches allowed when mapping probes to target sequences The value can be 0 or 1 or 2

Step 3: Enter email address

and

Step 4: Submit query

Since the process of generating remapped packages requires about 10 minutes, the results will not be available immediately after submission. Please enter a valid email address to receive alerts when results are ready.

AffyProbeMiner is a joint development of the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR) National Cancer Institute (NCI) and Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center. If you have any problems, questions or feedback on the tool, please email us.

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