Cbcb:Pop-Lab:Chris-Report

June 12, 2009

Tasks

Intergenic space and gene ontology work

• Investigated GO annotation tools that Bo has linked me to.
• I have been working on the Snail, Lottia gigantea, genome.
• Found the top 10% intergenic space with relative ease, however there was no GO annotation file for the genes. Most of the genomes of interest will not have a GO annotation file (shocker, I know).
• BLAST'd the sequences using Blast2GO, ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. http://www.blast2go.org/
• Blast2GO has a pipeline version, so I have been planning a way to take new incomplete genomes and have them run through this annotation pipeline.
• BLAST took around 8 hours for ~2200 sequences using an online database. I will run another group on the CBCB's BLAST.
• GO annotation using Blast2GO took around 24 hours.
• I plan on running HMMs for the approximate 200 sequences with no suitable hits this weekend.

Partition

• Drastically overhauling the backend of my partition program to make it more extendable/robust.
• Adding XML support to make parsing easier and increase possible functionality.
• Need to focus on getting James something usable asap.

Summer Goals

• Finish analyzing the intergenic space of the incomplete genomes. Determine future possibilities/publications.
• Modify/extend partition program to incorporate into James' metagenomic pipeline.
• Include viral metagenomic data into GeneParser.

Mar 2, 2009

Tasks

Intergenic space and gene ontology work with Cristian

• Approach

 Get the gene-spacing information - typically a simple parse of GFF files, if they are available.
 Get the gene function information - use GO if available.
 Rank the genes based on 5' spacing size.
 Take 10% longest, 10% shortest and middle 20% and find out what they do with GeneMerge

• Completed genomes
  • Anenome, Nematostella vectensis
  • Frog, Xenopus tropicalis
  • Waterflea, Daphnia pulex
• Incomplete genomes that require blast
  • Gastropod Snail, Lottia gigantea
  • Polychaete Worm, Capitella sp
• Future genomes
  • Leech, Helobdella robusta
  • Flatworm (Planaria), Schmidtea mediterranea
  • Sea Slug, Aplysia californica
  • Snail, Biomphalaria glabrata
  • Slime-mold, Dictyostelium purpureum QSDP1
• Waiting to hear back from Cristian about blast value cut-offs for incomplete genomes.

Partitioning System

• Splitting contigs based on "subgroup" information - essentially extending breaking up an entire assembly into multiple "sub-assemblies" each containing just reads from a single subgroup.

Conserved genomic elements in bacteria

• Update elements based on Adam's changes to Insignia.
• Find something to write about.

Interesting Stuff

• New insights into aging based on transcription factors, Prevailing theory of aging challenged in Stanford worm study