Hi, Wayne! You need to reverse complement your strand. The first good match on chr7 is on the - strand.
> NM_182762 6274 1 6276 6276 100.0% 7 - 20140804 20147092 6289 It is a nearly perfect match with two small gaps. Can you show us what command-line you used to run blat locally? thanks. -Galt On Fri, 26 Jun 2009, Wayne wrote: > Dear colleague, > > I did BLAT search for the following sequence > > >> NM_182762 6276 > AACAAAGCGUGUGUUUUUGAUGGGAGGGAAAAUGAGGUAAUGGUGUGUGU > GUGUGUGUGUCUGUGUGUGUCUGUGUGUGUCUCUGUGUGUCUGUGUGUGU > GUGUCUGUGUGUGUGUGUCUGUGUGUGUGUGUGUGUGUGUGUAGGAAAGA > AAGAAUCUCAGAAAAGCAUUAUAUUAAUUUUCUUCAUGCUCAAAACCAGU > UUUUUUUUCCUGAUGAAAGCACAGCCUAACUGAUAACCAAGAUGGGUUUU > AUCCUCAAAUAUGUAUUUUUGUGUAUGUUUCAAAUACAAGUAUUAGGCUG > CUUUGUUCUUAGAAAGGAAAGAAAAAAGAAAAGUGCCCUCUCUCUCUUUC > AGUGUUAUUUUAAAUUUACUAAGUCAAAGCUGUUUGAAUAAUUACAUCAC > ACAGAUAUCUGGGUAAACUAGAGACUAUCAACAUGAUCAAGGCAGUGUUC > CCAGGAGGCAGCUAGAAAGAGGGGAAGCAAGCACACACCCUGUGGCCAGU > CACGGCUGCCCGCUUUCCACACCUGACCUCUUCAGUUCAUCAGUGGGGUU > CACCAGCAUCACCCCCAUUUUUCAUGGGGAGAAACUCAGAAGUGGAGAGA > ACGUCUGAGGCUACAUAGCCAGUACAAAGUAGGUUUUCUGCUUGAAAAAC > CUGUUUCUAUUUCUUUUUAAAAAAUCAUACUGCAUAACAGAAUAGUAAAA > ACAAAAUGCGUGUUAAGACUUACAGGGAAACAGUUGCCGUUUCAUUUUAA > GUGAGACUUGCUACUCUUUUUCAUCGUCUCUUGAAAGACUGACAGAAGGA > AAAUAUGACUUAUCAGAAAUCUGUUGUCUGCAUGCAUGGACCUAGUGUUU > UCAUCAGCUCCCUUCAGCAUCUUGGGACCUCUCUAAUCCUGCCUAAUUUG > GGACUUUUUCUGCAGGAUUGUAAUGUAAAAUAGUUCUUUAGCUCUUGGAG > AUUUUUAAUAAUACGAGUUAUUAAAAACCACCACCACCAGAAACUUGAUU > AACUUGAUUACCCUGUUGAGUAGAGAGGUCUUAACCACCGAAAACACUGA > UAUCUUUAUGUUGGCAUGCUCAUGCAAACACAUGUGUGUGUGUGUGUGUG > UGUGUGUGUGUGUGUGUGUACCACAGUGUUUUAUAAAGCACAGCCUAAUU > GAUUAUAUAGGACAAAAAUUGUAUAGGACCCUGGGUCAGUAUAAAUGCUA > AUGGCUGACAAAGUUCACAAAGAGAUGUAUUUUGCUUACUCCUCUGUUCA > AUCCUCUGGUUGCCUGCCAGUGUUUAUGUGUGUAUUUGGACAGACAUUCA > UUUAUUGUCAUUCAGUCAAUAGGUAGAGUAUAUGUGUCUAUUUUUUGGCA > GGCAUAUAGAUGCUUGAGGCUAAUGGGAAAAAACCAGCAUGAACUCUGAC > UUUAGUAGUGCUAAGUAAUAGAUAAUUUUAAAAAAUGACACCGUUAAAUA > GAAAAUGGCAUGCAUACUAACAGUUGCAAUGGAGAGGCUGUGAUGCUACG > AGAUAUAAACGUAGAGAUGCCAUCAUGUGAAACUGGAAGUGGGGGUGGGU > CAGGGAAAUUUGUUCUUGGAAAGAAAUAAUGAACCUCAAGGAAGAGUAGG > CAUUGUCCUGGUGUGGUGGGGUGUAAGCGGUGAUCCCACAAAGCACUGAA > GCUCUUAGAUGGGUGGGAGCUGAAUAGGUGCAGAUAGCAGGGGUGAAGGA > GUGAAAGGAUAAAAGAUUCAAGGUUGAGAUGAGGAUGGAGCAAGAAGAAG > CCACAUUAGGGCCAUUAAGGCUGCUAGAAUUUAGAAAGAAAACACACAGC > CUCAAAGAAAUGUGGGUAAGCCAAAGAAGGAUUUUGUUUUGGGAACCUGA > AUAAAAGAUGUCCAUUUGGCUAAAAAGUAAAAGCAGAAUCUUUUUAGGGC > UUUUAAUAUACCCACCCUGGGAUAUUUGGUAUGCUGGCAAUGGUAAUUCA > AAUUGGCGUUUAAGAAUAAUCUUGGCCGGGCGCGAUGGCUCAUGCCUGAA > AUCCCAGCACUUUGGGAGGCCGAGGCGGGCAGAUCACUAGGUCAGGAGAU > CGAGACCAUCCUGGCUAACGCGGUGAAACCCCGUCUCUACUAAAAAUACA > AAAAAUUAGCCGGGCGUGGUGGCAGGCGCCUGUAGUCCCAGCUACUCAGG > AGGCUGAGGCAGGAGAAUGGCGUGAACCCGGGAGGCGGAGCUUGCAGUGA > GCCGAGUUCAUGCCACUGCACUCCAGCCUGGGUGACAGGCUGUCUCAAAA > AAAAAAAAAGGAAUAAUCUGUACGGCUUUCAGUAUUUAUAUUUGAUUAUA > AGGGAACACAGCCUGACCAAAUAAUUAUGUAUACACAUUCAAGGACAGAA > UUUAUUUUAAUUAAAAAUAAAUUAUGAGAGAAGGAAAAAAAAGCACAGUU > UUUACUUUCAGAACACAGUCCUUUUUUGUGGUGAUUUUGCUUUCUUUAGA > ACAUUCUUGGAAUCUUAUUAACAUGUCAGCUAACCAGAGAAUUUUGGGAA > GGGAUAGUGGGGAUUAAUAACUGGGUUUUUCCAGGCUCCAAGAUCUAAGA > AGACAGAGAUCUUGUUAGCUGAUUAGUGUAGUAAGAUUAAAUAAAUAAUU > UAAGGUUUACAUUGCAUCAUGUAUUAUGAUUGUGAUUGAGAAUAAUAAGA > GUUUAAAAAAAUGAAAAACAAGAUCUCUGUAAUUUGAGGAUGAAACAAUG > GUUCUAAUAUUAAUACACACAAAUAUAUUUUAUAAUCUUGUAACAAAUCC > UUCCAGGGGAAAUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUGAGCCAGA > GUCUGGCUCUGUUGCCCAGACUGGAGUGCGGUGUUUCAAUCUUGACUCAC > UGCAACCUCCACCUCCUGGGUUCAAAAGAUCCUUCUGCCUCCGCCUCCCA > AGUAGCUGGGAUUACAGGCAUGCACCACCUUGUCCGGGUAAUUUUUGUAU > UUUUAGUGGAGACAAGGUUUUACCAUUUUGGCCAGACUGGUCUGGAACUC > CUGACCUCAGGUCAUCCACCUGCCUCGGCCUCCCAGAGUGCUAGGAUUAC > AGGCAUGAGCCACUGCUCCCAGCCUUCCAGAGGAAUUUUAAGCCCAUGUC > CAAACAUUCUGUUUGUAUAAAUAUAUUCUAAUUUUUAAAUAAAUAGUUUC > UACUUUUCUGAACUUUAUAUUUUUUCUUGCUAUAAUGGAUUUUCAUAAUC > AGAAAAGAUUAAAUUAGUAAUCAUGAAUUGCCUUCAAUAUUUGGCAGUAA > GUCAAUGAAAUAAUAAGGCACUUAUAUACCAUCUUUGACAUCAUUAAAAG > UAUCAAAUCCCAUUAAUCUAAAACUUCUUUAAGCAUUUUGAAAGCAGAAA > AUGUUUACAUGGUUCUUUCAGUUCCUCAGGCUUUUUGUCUAAUGAUGCGU > GACUUAGGAUAAGAUUUGAAUUAAGUGCCCAGCUUGAAACAUAAUAAUUU > UUCUGUAUAAGCCACAGAUCCUCUACCUCCUUUGUGUUAAAGCCUUUAUA > UGAAACAAUUAAGUAGAAGCAUUCAAUAGUGUGUCAUUAACUGUUCAUAC > UAAUAAAUGGAUACAGCACAUUUUCAUGGCCUGUAAUGUAGAACAUACUA > UAUAAAGUUCUCAGUUUGGGGAUGACUAGGUUUCUGGAAGGAAUAGAAUG > CUAAAUCAAUGGAUGGCAUUGGGCUGAGAAACACUGCUGCUACUAAUCAG > CCUUGAAUGUGUAAUGUGAACAUGCAAAAGAGAACAUGCAUACACUCAAA > UUUGUACAAUGCUAUAACUGGAAGUUGAAGGACUUGAAUUUUUAUAUUGU > GCUAUUGUUAUGUUUUCUGUAAUUGUUUAUAUCUAAGGAAUUUUUGAGGU > AAUAUAAAAGAAAAAGAGAAUAAUGAACAAUGAUGUCACUGGAGGGUUUU > UACAUUAAAUUAGAUCAUUUUUCUUCUUAUUCACAAUAAUAAUCUUAAUC > UUUAAGAAUUAAUUAUAAUUUAAUAUUAUAAUUCAUAAUCUUUAAGAAUU > AAUAAUUAUAAUUUAAUAUUAUAAUUAAUAAUCUUUAAGAAUUAAUAAAU > AUUAUAAUUAAUAAUCUUUAAGAAUUAAUAAUUACAAUUAAUAAUUAAUA > AUAAUCUUAAUCUUUAAGAAUUAAUAAUAAUCCUUAAUCGCAAUAAUAAU > CGCAAGGAGGAGAAGUAAGUCCCUCCUCCUUCUGUAUGAACUUUUCUCCC > ACAUGCUGCUGUAUGGUUUAGUGAGAGUGAAGUUCUAAAGAACAUAUGAU > UGGUGGGAUAAUCCAAAGACAUUUUUUCAGAAUCAAAUGGCAUGUCGAAG > GUUUGUUUCUUGCAUAUGUAUUUACUGGUCCACAGCACAAAAUAAAGUGA > CCACAUAUACAUAGGAAAGUUGAAUUUGUACACAUACAGCAUCUGAAAUG > UAUCUGAUGUUCAGCAUCAAGAUUUCACUGAACAUUGUAGAAAUGUGUAU > CUUUUGCAUGUAUAUUUUACAUUGAUUUUCUAUUUAUGUACAUCUAGAAA > GUUUUAACCCUAAUAAAUAGUUUUGUAAUUUUGAAUAAUAGUGUCAGUUU > AUAUGUGAGGGAGUAGAGACAGAGAGGUUAGCACUGGAUAAUAAUUAGUA > AGGCCAAAGGAGAAAAUUUCAUAGAAAAUAUUGUUGUUGUCAUAAUGAGU > ACAGCAUGAAAGGCUUCCUCUACAAGACACUAGUCAAAGAGUUGAGAGCU > GCGGUUUCUAAUCUUUGUCCAUUACUCCCUUACUCCCUAUGAGACUGUGG > ACCUGUCACUUGGCCUCUCUGGUCUUCAGUUUUCUCACCAGUAAAACAAG > GAACUUGAACCAAAUGACCUCUAGUGUUCCCCUUGGGUUUAAAUGUCUAU > AAAUGUUCAAUGACUAGAAUGUAUUGCGUUUUUCUUUAUUCUUUUUGCUU > UGAGAAAAGAGAAUGUGAUUUAAGAGUAAUAAUUUGAAUACCAAUUAUCC > ACAUUAAAAUUGUGUCCUCUAUGUGUAAGGCAUAGCACAUUUAGCACACA > UACAUAAGCACACUAAGCACCUUACAAAUAUCCUCAUUUAUUCUUUACAU > AAUCUUUUGAAAUUGAUUAUGUAAUACACACUGUUUUUGAACAAUUGGUG > ACUUCCAGCUGUUUAAAACAAACUACAGUAUGGUGCUUGAGUACUGACUU > AGGAGGUCAGCAUUGGUUUCACUAGGAGCUUCUCAAAGCACGCUGCCAAA > CAUGCUCCAGUCUCAUUGUCAAGGCCUUAGACCAGGCAAUCAUUACGGCA > GUGGUUCUUCAACUUCAGCAGCAGCAAAACGAUCUGGCGGGGGCUUGGUG > AAACAGACUGCUGGGCUCGACCACCAGAAUUUCUCAUUCAGAGGGUCUGG > CCUGAUCACUUGCAUUUCUAAUCACUUCCCAGGUGAUGCAGAUGUUUCUG > GUCCAGGGACCCCAGUUUGAGAACCACUGUAUUAAAAUUUCCUUCAUCUC > UAUAGAAAUGGAAAGAUUUUUUAUAAGUCCUCUAAUUUGCUUUAAGAUAA > AUGAGAUUUCACUUAAUUCUGUUGGAGAAAUUGUUUUAAAAAUUGUGCUA > AAGAACCGAAAAUCACUUUAUGUUAAGGCUCUAUUUAUAGCAAGUGAACU > UUUCAUGAGUUAAUAAAGGCCUACAAAAAUAAUUUUGACUGUGAAACUAA > UUAAAAUCUCUGUGUUUCAUUUAAAGCAUAAACAUAUUUGAAUAAAAAUA > GGUUAACAAUAAUUUGGGACAUGUAUUCAGUAUAAUUUUAAGAUAAUUUU > ACAAAAUAUAUGUAACAUUGCAUUUGUUUCUGUAAAAUAUCUUCGGAAAA > AGCCUUGUUUUCCCUAGUGUGUUAUUUGUUGAAUUUCUUGUUAAAUGUAU > UUUUUCCCAUUGAAAAAAAUGUUUUUAAUCAAUGUGAUCAAUACAGCUAU > CUAUAUGCCCUGCUUUCACUGUAGAAUUAGAAAGUGUUAAUAAGGUGAUC > GGAUGUUCUUUCUAAGGAUCAUAUUCCACAUUUAAAGAGAUGGUGACUGA > GAAGAGGUGGCAAGCUGAACCAUCUCACUUUGAGAUUGACGUAUCACGUU > UUAUCCUCUGCCAUCAUUUCCUUGUUAAUUGUUUUUCUUUGGGUGAUUGG > AAGAAUCUAUGGCUUCCUUUUCUCUGUUCUUAAAGAUAUCAAGACUCUGC > CCUUUUGUGACUGGAAGUAGAUUUUAAAUGUCCCUAAUGUUUAUAUGCUC > ACUUAAACUCAAUACAUGGAAUUUACUGGGGCAUUUAACUUGUUCAUGAA > AAUAGAGUGAGUCAUUGAAAAAUCAA > > > in http://genome.ucsc.edu/cgi-bin/hgBlat (choose version hg18, Mar. 2006) > and the result is: > BLAT Search Results > > ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO > STRAND START END SPAN > --------------------------------------------------------------------------------------------------- > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:20140804-20147092&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=20140803&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=20140803&r=20147092&db=hg18&hgsid=136019191> > NM_182762 6274 1 6276 6276 100.0% 7 - 20140804 > 20147092 6289 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:116084102-116084394&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=116084101&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr11&l=116084101&r=116084394&db=hg18&hgsid=136019191> > NM_182762 248 1975 2259 6276 94.0% 11 - 116084102 > 116084394 293 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:16094573-16094880&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=16094572&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=16094572&r=16094880&db=hg18&hgsid=136019191> > NM_182762 241 1958 2259 6276 92.3% 7 - 16094573 > 16094880 308 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr9:130722169-130722454&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=130722168&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr9&l=130722168&r=130722454&db=hg18&hgsid=136019191> > NM_182762 236 1978 2254 6276 93.5% 9 + 130722169 > 130722454 286 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr14:68970544-69164800&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=68970543&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr14&l=68970543&r=69164800&db=hg18&hgsid=136019191> > NM_182762 228 2767 3077 6276 87.2% 14 + 68970544 > 69164800 194257 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr15:40192421-40192715&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=40192420&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr15&l=40192420&r=40192715&db=hg18&hgsid=136019191> > NM_182762 225 1975 2259 6276 91.9% 15 + 40192421 > 40192715 295 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr16:84335668-84335949&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=84335667&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr16&l=84335667&r=84335949&db=hg18&hgsid=136019191> > NM_182762 224 1986 2259 6276 92.5% 16 + 84335668 > 84335949 282 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr19:8494734-8495483&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=8494733&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr19&l=8494733&r=8495483&db=hg18&hgsid=136019191> > NM_182762 212 2776 3063 6276 88.6% 19 - 8494734 > 8495483 750 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr2:43841003-43841454&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=43841002&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr2&l=43841002&r=43841454&db=hg18&hgsid=136019191> > NM_182762 210 2772 3074 6276 84.9% 2 + 43841003 > 43841454 452 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr14:23473150-23473433&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=23473149&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr14&l=23473149&r=23473433&db=hg18&hgsid=136019191> > NM_182762 208 2782 3064 6276 87.0% 14 - 23473150 > 23473433 284 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr11:66605236-66605548&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=66605235&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr11&l=66605235&r=66605548&db=hg18&hgsid=136019191> > NM_182762 206 2773 3075 6276 85.9% 11 - 66605236 > 66605548 313 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr7:36341922-36342215&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=36341921&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr7&l=36341921&r=36342215&db=hg18&hgsid=136019191> > NM_182762 205 2782 3075 6276 90.6% 7 - 36341922 > 36342215 294 > browser > <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr17:17958281-17958582&db=hg18&ss=../trash/hgSs/hgSs_genome_362e_517790.pslx+../trash/hgSs/hgSs_genome_362e_517790.fa&hgsid=136019191> > details > <http://genome.ucsc.edu/cgi-bin/hgc?o=17958280&g=htcUserAli&i=../trash/hgSs/hgSs_genome_362e_517790.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_362e_517790.fa+NM_182762&c=chr17&l=17958280&r=17958582&db=hg18&hgsid=136019191> > NM_182762 205 2767 3066 6276 85.6% 17 + 17958281 > 17958582 302 > > However, when I did local BLAST research, I can not locate my query in the > same location in chromosome data (I downloaded Genome data from > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ > chromFa.zip<http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip>. > My local blast result showed that there is no perfect match in > chromosome > to my query). Furthermore, I tried to follow the BLAT result and locate my > query in chr7.fa manually. I found the sequence in position 20140804 is : > > TTGATTTTTCAATGACTCACTCTATTTTCATGAACAAGTTAAATGCC > CCAGTAAATTCCATGTATTGAGTTTAAGTGAGCATATAAACATTAGGGAC > ATTTAAAATCTACTTCCAGTCACAAAAGGGCAGAGTCTTGATATCTTTAA > GAACAGAGAAAAGGAAGCCATAGATTCTTCCAATCACCCAAAGAAAAACA > ATTAACAAGGAAATGATGGCAGAGGATAAAACGTGATACGTCAATCTCAA > AGTGAGATGGTTCAGCTTGCCACCTCTTCTCAGTCACCATCTCTTTAAAT > GTGGAATATGATCCTTAGAAAGAACATCCGATCACCTTATTAACACTTTC > TAATTCTACAGTGAAAGCAGGGCATATAGATAGCTGTATTGATCACATTG > ATTAAAAACATTTTTTTCAATGGGAAAAAATACATTTAACAAGAAATTCA > ACAAATAACACACTAGGGAAAACAAGGCTTTTTCCGAAGATATTTTACAG > AAACAAATGCAATGTTACATATATTTTGTAAAATTATCTTAAAATTATAC > TGAATACATGTCCCAAATTATTGTTAACCTATTTTTATTCAAATATGTTT > ATGCTTTAAATGAAACACAGAGATTTTAATTAGTTTCACAGTCAAAATTA > TTTTTGTAGGCCTTTATTAACTCATGAAAAGTTCACTTGCTATAAATAGA > GCCTTAACATAAAGTGATTTTCGGTTCTTTAGCACAATTTTTAAAACAAT > TTCTCCAACAGAATTAAGTGAAATCTCATTTATCTTAAAGCAAATTAGAG > > Obviously, this sequence is different from my query. > > So, my question is: Did I download the same version of genome data as used > in BLAT. If possible, could you please help me to explain why my local BLAST > result is different from your BLAT result? If I used the wrong data, could > you please tell me where to download the right one. > > Thanks beforehand. > > Regards > > Wayne > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
