You should use -out=psl (the default) if you want your results to match the web blat (hgBlat) closer.
A Psl is a full alignment containing chained-together-exons and gaps with splice-junction-adjusted. Blast output only contains exons with no gaps since that is all that the real BLAST program creates. When you chose blast output, the best single exon was on chr3, however the best full psl alignment is on chr7. QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN --------------------------------------------------------------------------------------------------- NM_005692.3 2235 1 2250 2262 100.0% 7 - 150535856 150555250 19395 NM_005692.3 1687 50 1982 2262 93.6% 3 + 88448934 88450861 1928 If you look at NCBI for NM_005692.3 http://www.ncbi.nlm.nih.gov/nuccore/27881504?report=GenBank it says that this mRNA is located on chr7. If you look at this one huge exon on chr3, it appears to be a processed-pseudogene. I offer my limited and simplistic understanding of pseudogenes: The introns are removed by splicing and then the now "processed" mRNA gets converted by some reverse transcriptase to DNA and then re-integrated into chr3. There may be other mechanisms that create processed pseudogenes as well. Some pseudogenes are expressed and retain expression, some lose expression, and some never had it. Unexpressed pseudogenes are more prone to decay via random mutation. Some pseudogenes turn into real functional genes and may evolve new uses. You can see that with the pseudo-gene tracks in the group Genes and Gene Prediction Tracks. -Galt On Wed, 15 Jul 2009, zhidong zhu wrote: > Dear UCSC Team: > > I build your blat system locally. When I run gfClient, I obtained a > different result from what I obtained from your web. How can I obtain the > identical result like your web supported. > The different points: > 1. the first match result: my local result chromosome is "chr3", while > your web result is "chr7" > 2. not perfect match occurred in my local result, while your web result > only shows 16 block perfectly match the chr7. > > My command: > ./gfClient 10.4.0.58 17779 ./ test_seq test_blast8 -t=rna -q=dna > -out=blast8 > > The content of test_blast8 is below: > gi|27881504|ref|NM_005692.3| gi|16|ref|chr3| 93.44 1935 118 3 > 50 1982 88448934 88450861 0.0e+00 3384.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 271 0 0 > 1980 2250 150536126 150535856 2.5e-152 535.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 213 0 0 > 266 478 150553007 150552795 1.8e-116 416.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 204 0 0 > 1642 1845 150543101 150542898 3.4e-112 402.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 196 0 0 > 70 265 150554519 150554324 4.3e-107 385.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 183 0 0 > 479 661 150552133 150551951 1.3e-99 360.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 172 0 0 > 662 833 150551868 150551697 1.7e-93 340.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 134 0 0 > 1846 1979 150542210 150542077 1.5e-70 263.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 129 0 0 > 1513 1641 150543751 150543623 5.7e-67 252.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 120 0 0 > 1129 1248 150546892 150546773 2.6e-62 236.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 111 0 0 > 1339 1449 150546210 150546100 1.6e-56 217.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 103 0 0 > 930 1032 150549699 150549597 2.0e-51 200.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 96 0 0 > 834 929 150550635 150550540 7.0e-48 188.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 96 0 0 > 1033 1128 150547178 150547083 1.0e-47 188.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 85.12 121 18 0 > 1843 1963 71206996 71207116 1.3e-45 181.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 86.21 116 16 0 > 1727 1842 71206141 71206256 1.8e-45 180.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 90 0 0 > 1249 1338 150546669 150546580 6.7e-44 175.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 69 0 0 > 1 69 150555250 150555182 1.5e-32 137.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 100.00 63 0 0 > 1450 1512 150544048 150543986 2.7e-28 123.0 > gi|27881504|ref|NM_005692.3| gi|20|ref|chr7| 93.75 32 2 0 > 1690 1721 71206102 71206133 8.0e-09 58.0 > > > zhidong zhu > national biochip engineering center at shanghai. > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
