Annotation of probes using annotated genome
0
0
Entering edit mode
8 months ago
kk.mahsa ▴ 140

Hi everyone

I am trying to annotate a set of probes (Affymetrix) for a plant species. I used blastn to find the desired genome region for each probe. But the results confused me. Now I have several hits (with the same parameters such as identity and evalue) for each probe. What should I do now? What is your suggestion to solve this problem?

blastn -task blastn-short -evalue 0.0001 -db plant_genes -query plant_affy_probes.fasta -out outputfile.csv -perc_identity 100 -outfmt 7
microarray probes affymetrix annotation blastn • 272 views
ADD COMMENT
0
Entering edit mode

it's been a while but if I remember correctly Affymetrix arrays uses probe-sets (== combination of multiple probes) to points a gene. So you need to combine several probes (or at least their hits on the genome) which will then , in most cases, point to a single gene. One probe can thus have several hits but the combination of probes should be more specific.

Why do you want/need to do this yourself btw? normally the array design comes with a file denoting to which gene the probes belong. (CDF file ?)

ADD REPLY
0
Entering edit mode

I use publicly available microarray data for meta-analysis. Plant species that I work on it have an annotated genome as the only source for probe set annotation. The annotation of probes in the Affymetrix site is very very poor and I have to use blast to the annotation of probes. How can I combine probes related to genes when I have no idea about it?

ADD REPLY
0
Entering edit mode

perhaps you can find some info in this publication (former colleagues of mine):

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-461

The array you use should in anyway come with a file denoting the probe set design of the manufacturer

ADD REPLY

Login before adding your answer.

Traffic: 1532 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6