Thanks Galt, I didn't bring up the strand issue, but it is good to point out. I don't think there is a problem - he is using masked sequence and web Blat uses unmasked (the last time I asked .....). But it is good that you are offering to help more. He may have something in his command that is causing a more significant change that can be accounted for by masking. I'll let you follow-up with the user - unless you specifically let me know to step in, so we don't confuse them with too many overlapping emails. Jennifer
Galt Barber wrote: > 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 > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
