[ensembl-dev] BLAT query enquire

Duarte Molha duartemolha at gmail.com
Mon Mar 2 15:45:44 GMT 2015


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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BLASTN 2.2.11 [blat]

Reference:  Kent, WJ. (2002) BLAT - The BLAST-like alignment tool

Query= 
         (60 letters)

Database: ensblat-04:30001 
           23 sequences; 3,000,000,000 total letters

Searching.done
                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

10                                                                     53   3e-07
10                                                                     45   8e-05
9                                                                      45   8e-05
17                                                                     43   3e-04
2                                                                      36   5e-02
14                                                                     35   7e-02



>10 
          Length = 135534747

 Score = 53 bits (138), Expect = 3e-07
 Identities = 38/44 (86%)
 Strand = Plus / Plus

Query: 18       tctttcttt-tttctttcttt---tctttctccctctctctctc 57
                ||||||| | ||||| |||||   ||||||||||||||||||||
Sbjct: 87328699 tctttctctctttctctctttctgtctttctccctctctctctc 87328742


 Score = 45 bits (116), Expect = 8e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

Query: 38       tctttctccctctctctctccct 60
                |||||||||||||||||||||||
Sbjct: 33933658 tctttctccctctctctctccct 33933680



>9 
          Length = 141213431

 Score = 45 bits (116), Expect = 8e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

Query: 38        tctttctccctctctctctccct 60
                 |||||||||||||||||||||||
Sbjct: 109840039 tctttctccctctctctctccct 109840061



>17 
          Length = 81195210

 Score = 43 bits (112), Expect = 3e-04
 Identities = 22/22 (100%)
 Strand = Plus / Minus

Query: 39       ctttctccctctctctctccct 60
                ||||||||||||||||||||||
Sbjct: 36111944 ctttctccctctctctctccct 36111923



>2 
          Length = 243199373

 Score = 36 bits (92), Expect = 5e-02
 Identities = 23/25 (92%)
 Strand = Plus / Minus

Query: 38        tctttctcc--ctctctctctccct 60
                 |||||||||  ||||||||||||||
Sbjct: 209893401 tctttctccctctctctctctccct 209893377



>14 
          Length = 107349540

 Score = 35 bits (91), Expect = 7e-02
 Identities = 18/18 (100%)
 Strand = Plus / Plus

Query: 40        tttctccctctctctctc 57
                 ||||||||||||||||||
Sbjct: 107208784 tttctccctctctctctc 107208801

  Database: ensblat-04:30001


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