[ensembl-dev] BLAT query enquire

[Duarte Molha]

anyone?

=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 2 March 2015 at 15:45, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear developers
>
> Please consider this genomic sequence:
>
> CTTTCTCTTTCTTTCTTTCTTTCTTTTTTCTTTCTTTTCTTTCTCCCTCTCTCTCTCCCT
>
>
> I got it from ensembl directly on GRCh37 on coordinates
> (X:153,795,306-153,795,365)
>
>
> Sequence export:
>
>
>
>
> http://grch37.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=X:153795306-153795365;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text
>
>
>
> However, if I blat this very same sequence on your own blat servers I get
> no perfect hit (please see attached text file).
>
>
> If, however, I blat it on UCSC blat servers I get 1 perfect matched hit at
> the expected coordinates:
>
> BLAT Search Results
>
>    ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
> ---------------------------------------------------------------------------------------------------browser <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153795306-153795365&db=hg19&ss=../trash/hgSs/hgSs_genome_2fc2_484490.pslx+../trash/hgSs/hgSs_genome_2fc2_484490.fa&hgsid=414875813_bYZ83pe63bElHH1MYpoaOoXfSIuQ> details <http://genome.ucsc.edu/cgi-bin/hgc?o=153795305&g=htcUserAli&i=../trash/hgSs/hgSs_genome_2fc2_484490.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_2fc2_484490.fa+YourSeq&c=chrX&l=153795305&r=153795365&db=hg19&hgsid=414875813_bYZ83pe63bElHH1MYpoaOoXfSIuQ> YourSeq           60     1    60    60 100.0%     X   +  153795306 153795365     60
>
>
> Can you explain the discrepancy?
>
> Best regards
>
> Duarte
>
>
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