./execAnno <project>

Contents

• Updating or redoing annotation
   
• Prune hits
  • Three methods
  • Use of GOs in pruning
  • Command line options for pruning
  • Comparison of prune results
  
  
• Save Database

1. Update to a newer AnnoDB (e.g. more recent UniProt release): In this case, you would delete existing annotation and all existing hit (tab) files.
2. Add a new AnnoDB: In this case, make sure to uncheck all annoDBs in the runSingleTCW interface that are already in the database.
3. Remove an annoDB: In this case, you will need to delete the existing annotation and reload all annoDBs that you want to keep. The original hit files can be reused.
4. Add additional similar pairs. In this case, turn off all other options and run Annotate; additional pairs will be added with the existing hit files.

The image on the right shows what can be removed. Select the top option for #1 and #3. Select the third item for the #1.

  ?--Annotation exists in database. Enter [a/d/e]
   Add to existing annotation [a], Delete annotation [d], Exit [e]:

The following is a flow for adding annotation from existing files.

  Checking annoDB fasta
    DB#1 diamond SP AA: projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta
    DB#2 blast SP AA: projects/DBfasta/UniProt_demo/sp_fullSubset/uniprot_sprot_fullSubset.fasta
    DB#3. blastn GB NT: projects/DBfasta/NT/dcitri.fa
    Pairs blastn: /projects/demoTra/hitResults/tra_seqNT.fa
    Pairs tblastx: /projects/demoTra/hitResults/tra_seqNT.fa
    Pairs diamond: /projects/demoTra/hitResults/tra_orfSeqAA.fa
 Checking for existing tab files

  ?--At least one hit tab file exists for selected set.
    Use current tab files [u], prompt on each tab file [p], exit[e]:  p

    DB#1 uniprot_sprot_plants.fasta
       Output exists: /projects/demoTra/hitResults/tra_SPpla.dmnd.tab; Date: Sun Jan 7 1:37:16 MST 2021
  ?--Load this existing file [y] or perform new search [n]  [y/n]:

If you get the prompt:

  ?--DB#1 The annoDB projects/DBfasta/UniProt_demo/sp_plants/uniprot_sprot_plants.fasta
     has been processed previously. Continue? (y/n)?

The default for this option is None, though the database queries are faster if pruning has been performed. If there is no reason to need all the hits, it is strongly recommended that you use the stringent Description option.

Prune: None

Prune: Alignment

tra_018  tr|A0A1S3CH76|A0A1S3CH76_CUCME  79.2  72..15..0..2..217..80..151..6.41e-33..117
tra_018  tr|A0A5A7SKQ5|A0A5A7SKQ5_CUCME  79.2  72..15..0..2..217..80..151..6.41e-33..117

The following is the results for tra_018.

Sometimes two hits can look identical from the Sequence Detail Hit Table, but the Show.. button shows all columns and will elucidate the differences (see Show A0A5A7SKQ5_CUCME). The hit start or hit end may be different, or the hit sequence lengths.

Prune: Description

  ZF-HD family protein {ORGLA09G0180300.1}
  ZF-HD family protein {ORGLA09G0074600.1}
  ZF-HD Family Protein

For both the Description and Alignment pruning:
   if two hits are being compared and found to be the same,
   if the GO database is defined and if two bit-scores are close,
   then the hit with the most GOs is saved.

For example, the following shows the top hits for tra_011, where Description pruning only keeps A0A0J8CG74_BETVU since its bit-score is just a little lower than A0A022Q8Q6_ERYGU and it has 2 GOs.

If it is desired to always use the best bit-score, do not define the GO database until after Annotate is run, then define the database and run GO only.

 -p Prune redundant hits  (annotation must already be done)
    -pt <integer> 1 Alignment  2 Descriptions   (this overrides what is set in Options)
    -pp <integer> Print first n pruned seq-hits per annoDB
    -pr Save/restore hit tables before processing

1. Using runSingleTCW, set the Prune option to None and check Ignore on Annotate. Run Annotate and exit.
2. View your database with all hits.
3. Run from the command line:

     ./execAnno demoTra -p -pt 1 -pp 4 -pr
   

   → The "-pr" options save the hits to two tables in the database prefixed with "save". It will then create the hits tables with pruning option of "Alignment".
   → The "-pp 4" option will print to the terminal the first 4 pruned hits per annoDB.
4. View your database with all the identical alignments per annoDB removed.
5. Run from the command line:

     ./execAnno demoTra -p -pt 2 -pp 4 -pr
   

   → The "-pr" option will notice that the saved tables exist and will restore them before continuing.
6. View your database with all the identical descriptions per annoDB removed.
7. The saved hit tables are still in the database; they will be removed when you remove annotation to re-annotate using runSingleTCW, or you can drop them using the mysql commands:

     drop table save_unique_hits;
     drop table save_unitrans_hits;
   

Further comparisons for Oryza sativa

→All terms are described on the Overview Reproduce popup, but briefly: Bits is the hit with the best bit-score for a sequence. Anno is the hit with the best annotation for a sequence. Rank=1 is the best hit for a sequence for an annoDB, e.g. if there are 6 annoDBs, a sequence has 6 Rank=1. → The Only, Bits, and Anno are about the same between the no pruning and description pruning. The Unique and Total are greatly reduced for the description pruning. → Right of Rank=1 refer to the Rank=1 hits. All numbers are just about the same between the no pruning and description pruning. → The high hitting species stay about the same for Bits and Anno, but the lower hitting species vary. →The Sequences with GOs reduced from 89% to 86%, but the Best hit with GOs (Best Bits) increased from 62.6% to 66.5%.

Overview with no pruning Overview with description pruning

  mysqldump -u <user> -p <database_name> > <dump_file_name>