HOW TO STORE BLAST RESULT INTO DATABASES?

Question

[sukeshssk]

I am comparing sequences with databases using NCBI command line blastall. Now, I wanted to store the results into Databases like SQL or Access or Whatever??????

Somebody will tell me, How to accomplish this task....

Thank You.

[Pierre Lindenbaum]

see also How To Capture The Blast Result In A String Variable To Save In A Database Using Bioperl

Answer 1

[Pierre Lindenbaum]

I wrote a XSLT stylesheet to put a BLAST+XML result into a sqlite database:

I wrote a xslt stylesheet transforming a BLASTN xml output to sqlite3 statements: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/blast2sqlite.xsl

usage:

xsltproc --novalid   blast2sqlite.xsl  blastn.xml |  sqlite3 blast.sqlite

sqlite> select * from Hsp limit 2;
         id = 1
     hit_id = 1
        num = 1
  bit_score = 57.9812
      score = 29.0
     evalue = 3.26022e-07
 query_from = 1
   query_to = 29
   hit_from = 122031912
     hit_to = 122031940
query_frame = 1
  hit_frame = 1
   identity = 29
   positive = 29
       gaps = 0
  align_len = 29
       qseq = GGACAGCGGTTGAGTCAGCCTGGGGAGAT
       hseq = GGACAGCGGTTGAGTCAGCCTGGGGAGAT
    midline = |||||||||||||||||||||||||||||

         id = 2
     hit_id = 1
        num = 2
  bit_score = 30.2282
      score = 15.0
     evalue = 73.7427
 query_from = 10
   query_to = 24
   hit_from = 86537689
     hit_to = 86537703
query_frame = 1
  hit_frame = 1
   identity = 15
   positive = 15
       gaps = 0
  align_len = 15
       qseq = TTGAGTCAGCCTGGG
       hseq = TTGAGTCAGCCTGGG
    midline = |||||||||||||||

[sukeshssk]

Sir, I am using Python and I am not having a knowledge of XLST.

Answer 2

[Mahmut Uludag]

Once BLAST output is generated in its json output format, it is easy to store these results in MongoDB or Elasticsearch. We have compiled our experience with storing BLAST results in Elasticsearch into an open-source project (https://github.com/uludag/hspsdb-indexer) which has brief documentation.