[BioC] visualization and alignment of affymetirx probe sequence to transcripts

shirley zhang shirley0818 at gmail.com
Tue Mar 24 17:08:05 CET 2009

Hi Bala,

Thanks for your information and sorry that I did not explain my
question very well.

Maybe my question is not about the alignment. For each gene, UCSC
browser gives you a set of probeset Ids and their location by clicking
Affymetrix expression track. For my purpose, for each gene, in
addition to probesets, can I add probe information in the track?
Please note that, here the probeset and probe information
(sequences/Ids) are from different platforms. For example, the
probeset/exon is from exon array, and the probe is from U133A array.


On Tue, Mar 24, 2009 at 11:40 AM, Balasubramanian Ganesan
<bala.g at aggiemail.usu.edu> wrote:
> Hi Shirley
> Many tools outside R are available to do this and are all free sequence
> alignment software. Check out any of Blast, T-Coffee, Muscle, or ClustalW.
> They are all quite simple to install and use (not all need installation;
> websites also provide interfaces for free). Blast at NCBI offers even web
> interfaces to align two sequences using its bl2seq program.
> Many, many more alignment tools are available. These four tools I have
> listed are some of the most popular and will definitely do what you want.
> On Mon, Mar 23, 2009 at 7:05 PM, shirley zhang <shirley0818 at gmail.com>
> wrote:
>> Dear List,
>> I have two sequences of transcripts (they are isoforms from one gene).
>> I would like to align affymetrix's exon sequences and probe sequences
>> to these two transcripts, and then visualize the alignment results.
>> What's the best way/tools to achieve this?
>> Thanks,
>> Shirley
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