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How To Build The Correct Blast Url For The Rest Interface

Hi All,

I am having difficulties constructing a BLAST query via the REST interface.

In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences.

The URL I construct is this (BTW, apparently the URL is to long for the forum): http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY_BELIEVE_DEFLINE=yes&QUERY=%3E%20PMID%2019846642%20Forward%0D%0AATGTTCGATTCCGGCTTCC%0D%0%3E%20PMID%2019846642%20Reverse%0D%0CGGGCTTCGGTGTACCTCAT&PROGRAM=blastn&DATABASE=nr&ENTREZ_QUERY=gyra%20[gene]%20AND%20AL123456.3%20AND%20txid83332%20[ORGN]&CMD=PUT

When I look at the query in the BLAST website interface, the Query Sequence looks like this:

>19846642 Forward
ATGTTCGATTCCGGCTTCCMDRVRSGGGCTTCGGTGTACCTCAT

What I really want is my Query to look like this:

>PMID 19846642 Forward
ATGTTCGATTCCGGCTTCC
>PMID 19846642 Reverse
GGGCTTCGGTGTACCTCAT

So it looks like the hex conversion somehow kinda worked but also kinda did not work.

What am I doing wrong in my query construction ?

blast
• 3,942 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by dgcatanzaro • dgcatanzaro

1 answer

my URL is 

$ curl -s "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=PUT&PROGRAM=blastn&DATABASE=nr&QUERY_BELIEVE_DEFLINE=false&ENTREZ_QUERY=gyra%20%5Bgene%5D%20AND%20AL123456.3%20AND%20txid83332%20%5BORGN%5D&QUERY=%3EPMID%2019846642%20Forward%0AATGTTCGATTCCGGCTTCC%0A%3EPMID%2019846642%20Reverse%0AGGGCTTCGGTGTACCTCAT%0A"

with QUERY_BELIEVE_DEFLINE=false : there is no gi on your fasta line:

it returns 

(...)
<!--QBlastInfoBegin
    RID = 59MF46VT01R
    RTOE = 20
QBlastInfoEnd
-->
(...)

I fetched the result with:

curl -s "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Get&RID=59MF46VT01R&FORMAT_TYPE=Text"


BLASTN 2.2.28+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro
A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and
David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new
generation of protein database search programs", Nucleic
Acids Res. 25:3389-3402.


RID: 59MF46VT01R


Database: Nucleotide collection (nt)
           20,069,287 sequences; 50,671,056,400 total letters
Query= PMID 19846642 Forward

Length=19
                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

emb|AL123456.3|  Mycobacterium tuberculosis H37Rv complete genome  35.6    3e-04

ALIGNMENTS
>emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome
Length=4411532

 Features in this part of subject sequence:
   DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydro...

 Score = 35.6 bits (38),  Expect = 3e-04
 Identities = 19/19 (100%), Gaps = 0/19 (0%)
 Strand=Plus/Plus

Query  1     ATGTTCGATTCCGGCTTCC  19
             |||||||||||||||||||
Sbjct  7476  ATGTTCGATTCCGGCTTCC  7494


 Features in this part of subject sequence:
   Probable medium chain fatty-acid-CoA ligase FadD14 (fatty...

 Score = 26.5 bits (28),  Expect = 0.14
 Identities = 14/14 (100%), Gaps = 0/14 (0%)
 Strand=Plus/Plus

Query  3        GTTCGATTCCGGCT  16
                ||||||||||||||
Sbjct  1181898  GTTCGATTCCGGCT  1181911


 Features in this part of subject sequence:
   Probable arsenic-transport integral membrane protein ArsB1

 Score = 26.5 bits (28),  Expect = 0.14
 Identities = 14/14 (100%), Gaps = 0/14 (0%)
 Strand=Plus/Minus

Query  5        TCGATTCCGGCTTC  18
                ||||||||||||||
Sbjct  3002143  TCGATTCCGGCTTC  3002130


 Features in this part of subject sequence:
   Possible lipid transfer protein or keto acyl-CoA thiolase...

 Score = 26.5 bits (28),  Expect = 0.14
 Identities = 14/14 (100%), Gaps = 0/14 (0%)
 Strand=Plus/Minus

Query  1        ATGTTCGATTCCGG  14
                ||||||||||||||
Sbjct  3959155  ATGTTCGATTCCGG  3959142


 Features in this part of subject sequence:
   Glutamine synthetase GlnA1 (glutamine synthase) (GS-I)

 Score = 24.7 bits (26),  Expect = 0.48
 Identities = 13/13 (100%), Gaps = 0/13 (0%)
 Strand=Plus/Plus

Query  6        CGATTCCGGCTTC  18
                |||||||||||||
Sbjct  2487721  CGATTCCGGCTTC  2487733


 Features in this part of subject sequence:
   Probable sugar-transport integral membrane protein ABC tr...

 Score = 24.7 bits (26),  Expect = 0.48
 Identities = 13/13 (100%), Gaps = 0/13 (0%)
 Strand=Plus/Plus

Query  6        CGATTCCGGCTTC  18
                |||||||||||||
Sbjct  2589020  CGATTCCGGCTTC  2589032


 Features in this part of subject sequence:
   Probable epoxide hydrolase EphC (epoxide hydratase)

 Score = 22.9 bits (24),  Expect = 1.7
 Identities = 12/12 (100%), Gaps = 0/12 (0%)
 Strand=Plus/Plus

Query  4        TTCGATTCCGGC  15
                ||||||||||||
Sbjct  1247372  TTCGATTCCGGC  1247383


 Features in this part of subject sequence:
   Probable Fmu protein (sun protein)

 Score = 22.9 bits (24),  Expect = 1.7
 Identities = 12/12 (100%), Gaps = 0/12 (0%)
 Strand=Plus/Minus

(...)

Query= PMID 19846642 Reverse

Length=19


                                                                   Score     E
Sequences producing significant alignments:                       (Bits)  Value

emb|AL123456.3|  Mycobacterium tuberculosis H37Rv complete genome  35.6    3e-04

ALIGNMENTS
>emb|AL123456.3| Mycobacterium tuberculosis H37Rv complete genome
Length=4411532

 Features in this part of subject sequence:
   DNA gyrase (subunit A) GyrA (DNA topoisomerase (ATP-hydro...

 Score = 35.6 bits (38),  Expect = 3e-04
 Identities = 19/19 (100%), Gaps = 0/19 (0%)
 Strand=Plus/Minus

Query  1     GGGCTTCGGTGTACCTCAT  19
             |||||||||||||||||||
Sbjct  7698  GGGCTTCGGTGTACCTCAT  7680


 Features in this part of subject sequence:
   Conserved hypothetical protein

 Score = 26.5 bits (28),  Expect = 0.14
 Identities = 14/14 (100%), Gaps = 0/14 (0%)
 Strand=Plus/Minus

Query  3        GCTTCGGTGTACCT  16
                ||||||||||||||
Sbjct  1029956  GCTTCGGTGTACCT  1029943



Lambda      K        H
   0.634    0.408    0.912 
Gapped
Lambda      K        H
   0.625    0.410    0.780 
Matrix: blastn matrix:2 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Sequences: 1
Number of Hits to DB: 0
Number of extensions: 0
Number of successful extensions: 0
Number of sequences better than 10: 0
Number of HSP's better than 10 without gapping: 0
Number of HSP's gapped: 0
Number of HSP's successfully gapped: 0
Length of database: 4411534
A: 0
X1: 22 (20.1 bits)
X2: 33 (29.8 bits)
X3: 110 (99.2 bits)
S1: 22 (21.1 bits)
• 122 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks ! I apparently did not realize what the definition line really is ! I thought it was basically a comment line but it can apparently be used as part of the algorithm.

• 0 views • link
written by dgcatanzaro • dgcatanzaro

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