Hello Juan, The browser PCR tool may be helpful. For serveral key species, the UCSC Genes are a searchable dataset along with the genomic sequence. http://genome.ucsc.edu/cgi-bin/hgPcr
Another option is to create a custom track containing the genomic coordinates of the probes. Then, in the Table browser, starting with the gene/mRna track of your choice, create an intersection filter, to pull out those sequences that align with overlap to the same genomic region as in your custom track. Or, send both datasets to Galaxy from the Table browser and perform the join there (better for multiple sequences and for knowing which probe pulled out which mRna sequence). The exact location will still be an unknown. Perhaps BLAT the probes against the smaller set of mRna sequences. Doing in batch is assuming that there is enough variation in your dataset to not cause cross-over alignments that are confusing to unravel. However, leaving them all together might be a good test to see if a probe is truly unique enough to be specific if you are focused on a certain gene family with homologous regions between the representatives (locations where you would not want a probe placed). Or, if using Galaxy, doing a 1-1 alignment between the probe and target mRna would be simple and specific (using the program of your choice, BLAT would be fine for probe sequences that are at least 25 bases long with near perfect identity - the longer the query sequence, the more mismatch allowed). There are several bioinformatics tools/wrapper utilities to do 1-1 alignments in batches - a quick google searches can find the latest versions - many open source. More information might be needed, maybe a GTF file with the regions of an mRna named (utr, exon, coding, non-coding, etc.) could be used along with the alignments to annotate the final alignment regions as to the region of the mRna matched. We hope this helps a bit, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Juan Dong" <[email protected]> wrote: > From: "Juan Dong" <[email protected]> > To: "[email protected]" <[email protected]> > Sent: Monday, November 9, 2009 3:42:05 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] (no subject) > > To Whom It May Concern, > > I have a probe sequences, and I have mapped to chromosomal location, > how can I find these sequences in the cDNA location? I have past the > sequences into the UCSC genome browser, there is no problem to find > their position in relation to the chromosomal location, but not to the > the cDNA location. Thanks > A_16_P17533794 H. sapiens > AAAAGCACGCAATTACCATTAACTAGTTAGATGTGCCATTGTAGAATAGGTAGAGGATCC > > chr6:46394321-46394380 A_16_P17533794 10143 > false RCAN2 ref|NM_005822 Homo sapiens regulator of calcineurin > 2 (RCAN2), mRNA. > > > Sincerely, > > Juan Dong > Instructor, > Institute of Oral Health Research > University of Alabama at Birmingham > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
