Download sequences of a set of Transcript clusters form Affimetrix

Question

[morgane.moreau]

Hi all,

I have a set of transcripts cluster IDs from Affimetrix (Human gene 1xST) and I would like to download the sequences to BLAST them. These have no annotations and I 'd like to find annotations where possible.

Does anyone know an easy way to download the sequences from a list of transcript ID ? I downloaded the transcripts and probesets CSV files but they do not contain the sequences. Is there another file that I didn't see that contain the sequences ?

At the moment I need to look for each cluster in Affimetrix, get the sequence, BLAST it, and start again for next cluster. Surely there is a better way to do that.

Any suggestion would be greatly appreciated.

Thank you,
Morgane

Answer 1

[morgane.moreau]

Never mind, I found out how to do it reasonably quickly.

For those who like me are starting with microarray and wonder:

You do a customize view in Affimetrix where you can select all the info you want about a cluster.

Then you do a batch query, download the file and BLAST all sequences at once.