Difference between revisions of "Load BLAST Into Chado"

From GMOD
Jump to: navigation, search
(Chado Tables Updated)
m (minor format changes)
Line 1: Line 1:
 
=Abstract=
 
=Abstract=
  
This HOWTO describes steps to add a BLAST analysis to a [[Chado_-_Getting_Started|Chado database]].
+
This [[:Category:HOWTO|HOWTO]] describes steps to add a [[:Category:BLAST|BLAST]] analysis to a [[Chado_-_Getting_Started|Chado database]].
  
 
=Have an existing Chado genome database =
 
=Have an existing Chado genome database =
  
See [[Load_RefSeq_Into_Chado|Load Refseq into Chado]] for advice on how to load a GenBank Genome into a database.
+
See [[Load RefSeq Into Chado]] for advice on how to load a GenBank Genome into a database.
In the following examples, '''bp_''scriptname''''' is from http://Bioperl.org/, and '''gmod_''scriptname''''' is from http://GMOD.org//.  As of this date (2007 April) you will need current modules from the BioPerl and GMOD CVS repositories to have this example work.
+
In the following examples, '''bp_''scriptname''''' is from [[BioPerl]], and '''gmod_''scriptname''''' is from GMOD.  As of this date (2007 April) you will need current modules from the BioPerl and [[CVS Access|GMOD CVS repositories]] to have this example work.
  
=Convert BLAST analysis to GFF=
+
=Convert BLAST analysis to GFF3=
  
For example, match yeast proteins to your genome with tBLASTn, and reformat to GFF v3.
+
For example, match yeast proteins to your genome with tBLASTn, and reformat to [[GFF3]].
  
 
   $ncbi/blastall -p tblastn -i MOD_Scer.fa -d dmel4 -o dmel4-modsc.tblastn
 
   $ncbi/blastall -p tblastn -i MOD_Scer.fa -d dmel4 -o dmel4-modsc.tblastn
 
+
 
First reformat to GFF with the Bioperl bp_search2gff.pl script.  The
+
First reformat to [[GFF3]] with the [[BioPerl]] <tt>bp_search2gff.pl</tt> script.  The Chado policy here is to put your program and blast query data names into the GFF3 <tt>--source</tt> field.  The GFF3 <tt>--method</tt> field should always be SO term 'match_part'.  You also want the <tt>--type hit</tt> and <tt>--target</tt> options.
Chado policy here is to put your program and blast query data names
+
into the GFF --source field.  The GFF --method field should always be
+
SO term 'match_part'.  You also want the --type hit and --target options.
+
  
 
   scripts/bp_search2gff.pl --in dmel4-modsc.tblastn \
 
   scripts/bp_search2gff.pl --in dmel4-modsc.tblastn \
 
       --out dmel4-modsc.tblastn.gff -version 3 \
 
       --out dmel4-modsc.tblastn.gff -version 3 \
       --format blast \  
+
       --format blast \
 
       --method match_part --source tBLASTn.MOD_Scer \
 
       --method match_part --source tBLASTn.MOD_Scer \
       --type hit --target  
+
       --type hit --target
  
Finally clean up the GFF a bit:
+
Finally clean up the GFF3 a bit:
  
 
   perl -pi -e 's/Target=Sequence:/Target=/' dmel4-modsc.tblastn.gff
 
   perl -pi -e 's/Target=Sequence:/Target=/' dmel4-modsc.tblastn.gff
  
==BLAST GFF sample for Chado==
+
==BLAST GFF3 sample for Chado==
  
 
Result should be formatted like this:
 
Result should be formatted like this:
 
+
<pre>
 
   ##gff-version 3
 
   ##gff-version 3
 
   # sample tBLASTn yeast protein x fly chromosome 4 (GenBank NC_004353) matches
 
   # sample tBLASTn yeast protein x fly chromosome 4 (GenBank NC_004353) matches
   # GFF formatted for loading to Chado database  
+
   # GFF formatted for loading to Chado database
 
+
 
 
   NC_004353 tBLASTn.MOD_Scer  match_part  141495  141815  48.9  - 0 Target=S000003211 43 156
 
   NC_004353 tBLASTn.MOD_Scer  match_part  141495  141815  48.9  - 0 Target=S000003211 43 156
 
+
 
 
   NC_004353 tBLASTn.MOD_Scer  match_part  161699  162793  217 + 0 Target=S000005817 984 1204
 
   NC_004353 tBLASTn.MOD_Scer  match_part  161699  162793  217 + 0 Target=S000005817 984 1204
 
   NC_004353 tBLASTn.MOD_Scer  match_part  160517  161407  185 + 0 Target=S000005817 455 980
 
   NC_004353 tBLASTn.MOD_Scer  match_part  160517  161407  185 + 0 Target=S000005817 455 980
 
     # this is a protein match with 2 HSP parts, note the identical Target=
 
     # this is a protein match with 2 HSP parts, note the identical Target=
 +
</pre>
  
 
=Load Query Protein sequence to Chado DB=
 
=Load Query Protein sequence to Chado DB=
  
You want to have your query sequences used for BLAST,  
+
You want to have your query sequences used for BLAST, such as proteins, for reference in your [[Chado]] db.  The GMOD script <tt>gmod_bulk_load_gff3.pl</tt> will handle this after converting sequence Fasta to [[GFF3]] format.
such as proteins, for reference in your Chado db.  The
+
GMOD Bulk_load_gff3 will handle this after converting
+
sequence Fasta to GFF format.
+
  
   gmod_fasta2gff3.pl  --type protein --source SGD --fasta MOD_Scer.fa --gff MOD_Scer.fa.gff  
+
   gmod_fasta2gff3.pl  --type protein --source SGD --fasta MOD_Scer.fa --gff MOD_Scer.fa.gff
 
   gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism yeast --dbxref --gff MOD_Scer.fa.gff
 
   gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism yeast --dbxref --gff MOD_Scer.fa.gff
  
If your query sequence comes from UniProt or GenBank formats,
+
If your query sequence comes from UniProt or GenBank formats, you can instead use the <tt>[[Load GFF Into Chado | bp_genbank2gff.pl]]</tt> script that will retain more useful annotations for your Chado database.  Then BLAST matches can
you can instead use the [[Load_GFF_Into_Chado | bp_genbank2gff.pl]] script that will retain more  
+
useful annotations for your Chado database.  Then BLAST matches can
+
 
be linked to many known gene/protein attributes.
 
be linked to many known gene/protein attributes.
  
=Load BLAST result GFF to Chado DB=
+
=Load BLAST result GFF3 to Chado DB=
  
Use the GMOD Bulk_load_gff3 script for this, indicating the
+
Use the <tt>gmod_bulk_load_gff3.pl</tt> script for this, indicating the
input is --analysis, and the Target names are unique IDs matching
+
input is <tt>--analysis</tt>, and the Target names are unique IDs matching
 
above protein features.
 
above protein features.
  
 
   gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism fruitfly \
 
   gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism fruitfly \
 
     --analysis --unique_target --score raw  \
 
     --analysis --unique_target --score raw  \
     --gff dmel4-modsc.tblastn.gff  
+
     --gff dmel4-modsc.tblastn.gff
  
 
Note: If you have pre-loaded the database with all the protein
 
Note: If you have pre-loaded the database with all the protein
 
sequence features such as the SGD:S000002445 protein, you should use
 
sequence features such as the SGD:S000002445 protein, you should use
'gmod_bulk_load_gff3 --analysis --unique_target' to ensure that Target
+
gmod_bulk_load_gff3 --analysis --unique_target
feature is linked with your Blast result.
+
to ensure that Target feature is linked with your Blast result.
  
 
==Chado Tables Updated==
 
==Chado Tables Updated==
Line 114: Line 107:
  
 
=Authors=
 
=Authors=
+
 
 
* [[User:Dongilbert|Dongilbert]] 23:24, 3 April 2007 (EDT)
 
* [[User:Dongilbert|Dongilbert]] 23:24, 3 April 2007 (EDT)
  

Revision as of 19:50, 30 December 2008

Abstract

This HOWTO describes steps to add a BLAST analysis to a Chado database.

Have an existing Chado genome database

See Load RefSeq Into Chado for advice on how to load a GenBank Genome into a database. In the following examples, bp_scriptname is from BioPerl, and gmod_scriptname is from GMOD. As of this date (2007 April) you will need current modules from the BioPerl and GMOD CVS repositories to have this example work.

Convert BLAST analysis to GFF3

For example, match yeast proteins to your genome with tBLASTn, and reformat to GFF3.

 $ncbi/blastall -p tblastn -i MOD_Scer.fa -d dmel4 -o dmel4-modsc.tblastn

First reformat to GFF3 with the BioPerl bp_search2gff.pl script. The Chado policy here is to put your program and blast query data names into the GFF3 --source field. The GFF3 --method field should always be SO term 'match_part'. You also want the --type hit and --target options.

 scripts/bp_search2gff.pl --in dmel4-modsc.tblastn \
     --out dmel4-modsc.tblastn.gff -version 3 \
     --format blast \
     --method match_part --source tBLASTn.MOD_Scer \
     --type hit --target

Finally clean up the GFF3 a bit:

  perl -pi -e 's/Target=Sequence:/Target=/' dmel4-modsc.tblastn.gff

BLAST GFF3 sample for Chado

Result should be formatted like this:

  ##gff-version 3
  # sample tBLASTn yeast protein x fly chromosome 4 (GenBank NC_004353) matches
  # GFF formatted for loading to Chado database

  NC_004353 tBLASTn.MOD_Scer  match_part  141495  141815  48.9  - 0 Target=S000003211 43 156

  NC_004353 tBLASTn.MOD_Scer  match_part  161699  162793  217 + 0 Target=S000005817 984 1204
  NC_004353 tBLASTn.MOD_Scer  match_part  160517  161407  185 + 0 Target=S000005817 455 980
     # this is a protein match with 2 HSP parts, note the identical Target=

Load Query Protein sequence to Chado DB

You want to have your query sequences used for BLAST, such as proteins, for reference in your Chado db. The GMOD script gmod_bulk_load_gff3.pl will handle this after converting sequence Fasta to GFF3 format.

 gmod_fasta2gff3.pl  --type protein --source SGD --fasta MOD_Scer.fa --gff MOD_Scer.fa.gff
 gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism yeast --dbxref --gff MOD_Scer.fa.gff

If your query sequence comes from UniProt or GenBank formats, you can instead use the bp_genbank2gff.pl script that will retain more useful annotations for your Chado database. Then BLAST matches can be linked to many known gene/protein attributes.

Load BLAST result GFF3 to Chado DB

Use the gmod_bulk_load_gff3.pl script for this, indicating the input is --analysis, and the Target names are unique IDs matching above protein features.

 gmod_bulk_load_gff3.pl --dbname my_chado_01  --organism fruitfly \
   --analysis --unique_target --score raw  \
   --gff dmel4-modsc.tblastn.gff

Note: If you have pre-loaded the database with all the protein sequence features such as the SGD:S000002445 protein, you should use

gmod_bulk_load_gff3 --analysis --unique_target

to ensure that Target feature is linked with your Blast result.

Chado Tables Updated

Then you should see these database updates:

   Analysis table entry of the Chado_Companalysis_Module:
 analysis_id|name|description|program|programversion|algorithm|sourcename|.
 10|tBLASTn.MOD_Scer||tBLASTn|null||MOD_Scer|
   Analysisfeature table entries (1/hsp)
 analysisfeature_id|feature_id|analysis_id|rawscore|normscore|significance|identity
 21|88148|10|117|||    << 1st HSP
 22|88150|10|91.7|||
 ...
   Feature table entry for Hit feature_id 88148 :
 dev_chado_01b=# select * from feature where feature_id = 88148;
 feature_id|dbxref_id|organism_id|name|uniquename|residues|seqlen|md5checksum|type_id|is_analysis|is_obsolete|
 88148|76797|10|protein_match-auto88148|auto88148||||423|t|f|
 ...
   Featureloc entries for Hit feature_id 88148:
 featureloc_id|feature_id|srcfeature_id|fmin|is_fmin_partial|fmax|is_fmax_partial|strand|phase|residue_info|locgroup|rank
 88149|88148|88149|69|f|858|f||||0|1        << Target protein
 88148|88148|31118|24052|f|24448|f|1|||0|0  << Source genome
   Featureloc entries for Target feature_id 88149:
 88149|88148|88149|69|f|858|f||||0|1  -- first HSP
 88151|88150|88149|69|f|858|f||||0|1  -- second HSP

I believe the ranks shown in the featureloc example above may not be correct or at least are misleading; see the Chado Best Practices section for handling BLAST results for clarification Scott 19:18, 21 November 2008 (UTC)

See also

More Information

Please send questions to the GMOD developers list:

gmod-devel@lists.sourceforge.net

Authors