Adding GO GO Workshop 3-6 August 2010

1. GOanna results and GOanna2ga 2. gene association files 3. getting GO for your dataset 4. adding more GO (introduction) 5. requesting GO

 only returns existing GO  only accepts limited accession types  GOanna does a Blast search against existing GO annotated products.  allows you to quickly transfer GO to gene products where they have similar sequences  accepts fasta files

Incorrect address – you will not receive your results! Contact AgBase if you have not received results after 24-48h.

Standard BLAST parameters

default setting

GOanna Results If you enter an incorrect address – you will not receive your results! Contact AgBase if you have not received results after 24-48h.

query IDs are hyperlinked to BLAST data (files must be in the same directory)

*WHAT IS A GOOD ALIGNMENT? 1. Manually inspect alignments and delete any lines where there is not a good alignment*. 2. Add this additional annotation to the annotations from GORetriever.

GOanna2ga New to AgBase: an online script to convert your GOanna file to a gene association file format. add manually checked GOanna annotations to a GORetriever file

Tutorial 4: adding GO using GOanna For this example, we will use a list of NCBI Cassava proteins that have no GO annotation.  4.1 Example 1: Cassava GOanna GOanna2ga  4.2 Example 2: Working on your own data Add GO to a sample from your own data set. Alternatively, use GOanna to add GO to the file of accessions from tutorial 2 that had no GO.  We will continue to work on this tomorrow.

Requesting GO

Some limitations of GOanna: BLAST analysis is slow – results ed limit to 1,000 sequences/submission limit to 3 jobs submitted/user at one time limit of <3 databases selected for any one job How do I do to get GO for my 50,000 RNA-Seq dataset?  50 x GOanna submissions + manual interpretation of results – impractical and slow!!  ALTERNATIVELY: Contact AgBase  we use internal GO annotation pipelines  GO can be kept private and released after publication.

Tutorial 4: adding GO using GOanna For this example, we will use a list of NCBI Cassava proteins that have no GO annotation.  4.1 Example 1: Cassava GOanna GOanna2ga  4.2 Example 2: Working on your own data Add GO to a sample from your own data set. Alternatively, use GOanna to add GO to the file of accessions from tutorial 2 that had no GO.  We will continue to work on this tomorrow.