Hi, Medha
If you want to align mRNA using hgBlat, please choose "DNA" from the Query Type dropdown list. Most of your questions stem from the use of translated blat, which it appears you have no reason to use. Translated blat is used when the evolutionary distance is so great that dna matches no longer work. If you are doing a regular mRNA alignment you are probably aligning to the same species and thus translated blat is irrelevant. When using blat for dna to dna searches, there is no difference between -q=rna and -q=dna. You get exactly the same result. The distinction only matters for translated searches. -Galt 6/7/2011 11:20 AM, Bhagwat, Medha (NIH/OD/ORS) [E]: > 1. What is the Query type RNA? How it differs from DNA? It seems to be > available in standalone but not on web. > > 2. http://genome.ucsc.edu/goldenPath/help/blatSpec.html mentions > > Mapping full length mRNAs to the genome in the same species > -ooc=11.ooc -fine -q=rna > > So what is the best query type for mRNA query on the web? > > > 3. I read the response in the Archives > Re: BLAT - The meaning of translated DNA/RNA > Date: 2010-04-19 > but still not clear to me translated RNA and translated DNA types. I > understand one is 3 frame translation and other is 6 frame translation. What > is meant by "stranded" and "no strand info" mentioned in the response. When > I run mRNA (cDNA) sequence on the web, I do get strand information for both > types. > > > 4. I read FAQs. But it is still not clear to me what are the exact > parameters used on the web. How do I get that list? > > Thanks, > > Medha > _____________________________ > Medha Bhagwat, PhD > Informationist/Bioinformatics Specialist > NIH Library > National Institutes of Health > Building 10, Room 1L13F > 10 Center Drive > Bethesda, Maryland 20892-1150 > T. 301-496-2185 > F. 301-402-0254 > E. [email protected] > http://nihlibrary.nih.gov > http://nihlibrary.nih.gov/bioinformatics > _____________________________ > Amazing Research. Amazing Help. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
