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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.

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Adding GO

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  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.

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