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. Thanks, Shirley 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. > BALA. > > 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >