Report3

Mar 27,2009

OBJECTIVE:

Find gene/protein homologs and provide functional annotation for our sets of assembled EST contigs and singlets from our two sea urchin species under investigation – H. erythrogramma and H. tuberculata.

PROCEDURE:

As shown in the chart above, we first ran our contigs and singlets generated for each species by ESTPiper through the GLIMMER program to identify the most likely ORF (reading frame, start and stop position) for each sequence. We then extracted the specified nucleotide sequences predicted to be genes from the raw contig or EST sequences, and then translated the nucleotide sequences to an amino acid sequences.

Next, we took these sets of amino acid sequences and ran BLAST searches (using blastp) against the NR protein database. We took the sequences with BLAST hits and used these as the inputs to PFP and KAAS (programs described below).

PFP generated a list of most probable GO terms for each input sequence. We took the top five most probable (determined by p-value) GO terms from each ontology (b – biological process, f – molecular function, c – cellular component) and generated summary tables of these predictions. We also fed the predicted GO terms from PFP through CateGOrizer to consolidate and summarize the GO term predictions for each species (using the GO Slim ontologies).

KAAS generated a list of hits to KOs (KEGG orthologs) along with KEGG network hierarchy summaries and pathway maps for all sequences with KO matches.

Result:

PFP

• H. erythrogramma
  • Top 5 GO terms for each contig and singlet
  • Summary of GO terms from CateGOrizer
    • GO Root (biological process / molecular function / cellular component)

    

    • GO Slim summary (all GO Slim terms)
• H. tuberculata
  • Top 5 GO terms for each contig and singlet
  • Summary of GO terms from CateGOrizer
    • GO Root (biological process / molecular function / cellular component)

    

    • GO Slim summary (all GO Slim terms)

KAAS

• H. erythrogramma
  • KAAS output
• H. tuberculata
  • KAAS output

Contributions:

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