1 / 22

Adding GO

Adding GO. GO Workshop 3-6 August 2010. GOanna results and GOanna2ga gene association files getting GO for your dataset adding more GO (introduction) requesting GO. only returns existing GO only accepts limited accession types.

snowy
Download Presentation

Adding GO

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Adding GO GO Workshop 3-6 August 2010

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

  3. 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

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

  5. Standard BLAST parameters

  6. default setting

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

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

  9. 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. *WHAT IS A GOOD ALIGNMENT?

  10. 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

  11. 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 • 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.

  12. Requesting GO

  13. 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.

  14. 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 • 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.

More Related