Frequently Asked Questions

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What is a probe?
A probe is short piece of DNA from with a specific target in the genome. Probes are usually representative of a specific gene, but sometimes target mRNAs, ESTS, or other areas of interest in a genome. A probe id is a unique identifier of a probe on a specific array.

This paper XXX outlines the annotation process in depth. Put briefly, we use the manufacturers probe sequence (or in the case of Affymetrix, the probe group target sequence) to find a genomic coordinate. We use the top result from this analysis as long as it has greater than 98% identity to the genome. We also place the position of the probe within the sequence it was originally designed for (e.g. a REFSEQ sequence) and position this on the genome as well. This helps place the probe properly in the cases where thereare multiple genomic matches (which are reported as multiple)

How do you determine what gene, mRNA, or EST a probe targets?
Once we have the genomic coordinates of the probe, we compare this position to all the UCSC known genes. If the probe's location exists within or partly within any of a gene's many exons, we determine the probe a target of the gene. If the probe does not appear to target any of the genes known by UCSC, we examine all of the UCSC mRNAs of a match in the same fashion; if stil there is no match, we examine UCSC's known ESTs for a match. Once we have matched probes to transcripts in this fashion, we can use this information to identify probes from any manufacturer that also matches the same entity.

How often do you update your databases?
Keeping all databases concurrent and up to date on a daily basis is essentially impossible. One of the reasons for this is because publicly available data sources are dynamically moving objects and never updated synchronously at their respective sources. It also takes a few days for us to construct all the intermediate tables linking all the information. We have decided to do quarterly updates of the ArrayTrans database, and if you check our database statistics section, you will see the versions of all the data sources.

Why is the advanced search limited to 200 probes per query?
If you are searching this many probes, you should download the whole array comparison from the whole array search page.

How do I interpret a genomic location or BLAT result?
The BLAT result is displayed as 'chrom:chromStart-chromEnd'. chrom is the name of the chromosome. The first base in a chromosome is numbered 0. chromStart is the start position of the BLAT result, and chromEnd is the end position of the BLAT result. The chromEnd base is NOT included in the hit. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100. The relative location of the probe within the bounds of a gene (or mRNA/EST) is illustrated by blue (for negative strand coding genes) or red (for positive strand coding genes) bars. Clicking on the location of a probe brings you to the UCSC browser where you can see exactly where the probe is located.