Adding GO

GO Workshop3-6 August 2010

1. GOanna results and GOanna2ga2. gene association files3. getting GO for your dataset4. 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 email address – you will not receive your results!

Contact AgBase if you have not received results after 24-48h.

Standard BLAST parameters

default setting

GOanna ResultsIf you enter an incorrect email 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.

GOanna2gaNew 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 GOannaFor this example, we will use a list of NCBI Cassava proteins that have no GO annotation. 4.1 Example 1: Cassava

4.1.1 GOanna 4.1.2 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 emailed• 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 GOannaFor this example, we will use a list of NCBI Cassava proteins that have no GO annotation. 4.1 Example 1: Cassava

4.1.1 GOanna 4.1.2 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.