Hello Hannah, The self-chain uses blastz to make it's alignments. You can see the method here: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=chainSelf
BLAT is a different aligner and so will align different things than blastz does. This is not an error. There is no one correct alignment between any two DNA sequences because the different aligners don't know the real history of the DNA segments in question. It is up to the researcher to choose an alignment that they think is the best one based on their understanding of the region in question, and the general behavior of their chosen aligner. I hope this answers your question. If you have follow up questions, please post them to this list. Brian On Thu, Feb 3, 2011 at 2:04 PM, Cheung, Hannah <[email protected]> wrote: > To Whom It May Concern, > > How do the BLAT and Self-Chain algorithms differ? The reason I ask is shown > below. > In trying to look at differences among the MHC haplotypes, I did a BLAT > search on the following sequence: > >>seq1 > ACAGACCCCAGCTTTACAAGGACCCCAGCTCCTTAACACAGATCCCAGCTCCGAGGAAACTCGTCCCCCCCACGTTAATCCTGACCGACTTTGCCACATG > BLAT Search Results > > ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND > START END SPAN > --------------------------------------------------------------------------------------------------- > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_mann_hap4:2454805-2454904&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2454804&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6_mann_hap4&l=2454804&r=2454904&db=hg19&hgsid=185182739> > YourSeq 100 1 100 100 100.0% 6_mann_hap4 + 2454805 > 2454904 100 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_dbb_hap3:2403575-2403674&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2403574&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6_dbb_hap3&l=2403574&r=2403674&db=hg19&hgsid=185182739> > YourSeq 100 1 100 100 100.0% 6_dbb_hap3 + 2403575 > 2403674 100 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_cox_hap2:2621159-2621258&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2621158&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6_cox_hap2&l=2621158&r=2621258&db=hg19&hgsid=185182739> > YourSeq 100 1 100 100 100.0% 6_cox_hap2 + 2621159 > 2621258 100 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:31106437-31106536&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=31106436&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6&l=31106436&r=31106536&db=hg19&hgsid=185182739> > YourSeq 100 1 100 100 100.0% 6 + 31106437 31106536 > 100 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_mcf_hap5:2488382-2488481&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2488381&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6_mcf_hap5&l=2488381&r=2488481&db=hg19&hgsid=185182739> > YourSeq 98 1 100 100 99.0% 6_mcf_hap5 + 2488382 > 2488481 100 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_qbl_hap6:2402283-2402381&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2402282&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr6_qbl_hap6&l=2402282&r=2402381&db=hg19&hgsid=185182739> > YourSeq 96 1 100 100 96.0% 6_qbl_hap6 + 2402283 > 2402381 99 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr17:8526697-8526717&db=hg19&ss=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+../trash/hgSs/hgSs_genome_a22_b1d170.fa&hgsid=185182739> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=8526696&g=htcUserAli&i=../trash/hgSs/hgSs_genome_a22_b1d170.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_a22_b1d170.fa+YourSeq&c=chr17&l=8526696&r=8526717&db=hg19&hgsid=185182739> > YourSeq 21 22 42 100 100.0% 17 - 8526697 8526717 > 21 > > > > > The MANN (6_mann_hap4) result shows a perfect alignment. > The QBL (6_qbl_hap6) result shows one polymorphism and one insertion. > > Next, I did a BLAT on a subset of this sequence that includes the > polymorphism and insertion sites: >>seq2 > CCGAGGAAACTCGTCCCCCCCGTTAATCCTGACCGACTT > > BLAT Search Results > > ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND > START END SPAN > --------------------------------------------------------------------------------------------------- > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_mann_hap4:2454855-2454895&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2454854&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6_mann_hap4&l=2454854&r=2454895&db=hg19&hgsid=185185025> > YourSeq 38 1 39 39 100.0% 6_mann_hap4 + 2454855 > 2454895 41 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_dbb_hap3:2403625-2403665&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2403624&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6_dbb_hap3&l=2403624&r=2403665&db=hg19&hgsid=185185025> > YourSeq 38 1 39 39 100.0% 6_dbb_hap3 + 2403625 > 2403665 41 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_cox_hap2:2621209-2621249&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2621208&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6_cox_hap2&l=2621208&r=2621249&db=hg19&hgsid=185185025> > YourSeq 38 1 39 39 100.0% 6_cox_hap2 + 2621209 > 2621249 41 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6:31106487-31106527&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=31106486&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6&l=31106486&r=31106527&db=hg19&hgsid=185185025> > YourSeq 38 1 39 39 100.0% 6 + 31106487 31106527 > 41 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_qbl_hap6:2402333-2402372&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2402332&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6_qbl_hap6&l=2402332&r=2402372&db=hg19&hgsid=185185025> > YourSeq 36 1 39 39 97.5% 6_qbl_hap6 + 2402333 > 2402372 40 > browser<http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr6_mcf_hap5:2488432-2488472&db=hg19&ss=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+../trash/hgSs/hgSs_genome_1458_b24af0.fa&hgsid=185185025> > > details<http://genome.ucsc.edu/cgi-bin/hgc?o=2488431&g=htcUserAli&i=../trash/hgSs/hgSs_genome_1458_b24af0.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_1458_b24af0.fa+YourSeq&c=chr6_mcf_hap5&l=2488431&r=2488472&db=hg19&hgsid=185185025> > YourSeq 34 1 39 39 94.9% 6_mcf_hap5 + 2488432 > 2488472 41 > > > This time: > > The MANN result shows me a deletion of AC. > > The QBL result shows me that the polymorphism is present, but that there is a > deletion rather than an insertion 8 bp away from the polymorphism site. > > Furthermore, the Self-Chain alignment within the MANN result shows that the > QBL has a different base deleted than the one shown in the QBL result. > > Why the discrepancies? > > > > Sincerely, > > Hannah Cheung, PhD > Postdoctoral Associate > Plon Lab > 1102 Bates Ave > Rm.1200.18 > Texas Children's Hospital > Houston, TX 77030 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
