[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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