Hi Nicholas, Yes, Blat is the alignment tool that we have here at UCSC. Please note that there are several limitations to our web based blat, one of which is, "only DNA sequences of 25,000 or fewer bases and protein or translated sequence of 10000 or fewer letters will be processed." Since you have sequences longer than that, you would have to break them into chunks of <= 25,000 to process them. For more info, please read the Blat page, http://genome.ucsc.edu/cgi-bin/hgBlat.
You could download blat yourself to get around the 25k limit. Here are some instructions on downloading and using blat: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads Finally, BLAT might not be the best tool for aligning genomic sequence (it was designed to quickly align mRNA sequence to the genome). You might want to check out Blast: http://blast.ncbi.nlm.nih.gov/Blast.cgi - Greg Roe UCSC Genome Browser On 2/5/11 3:27 PM, Nicholas Price wrote: > Hi > > I have the sequences of the unspliced human genes and I want to run a > homology search against the human genome that excludes any gene coding > regions. > Using UCSC is Blat the only option? and if so how could I use it to > analyse a large number of sequences that can be 75000 nuclotides long? > > Nicholas > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
