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.