Moore Notes 4 1 09
From OpenWetWare
Jump to navigationJump to search
Group Call
- Progress Report was due Monday (now Friday)
- OK if not much to add since annual report
- JE will start wiki page
- We should all add what we're up to (~ paragraph per postdoc, plus sections on presentations, pubs, etc)
- Simulations
- Do we have a place to put data/code set up yet?
- Every one needs to send their logins to Srijak
- format for alignments (Stokholm?)
- Dongying has alignmentformt.pl script
- Martin uses E-entrance from NCBI
- profile HMMs from AMPHORA
- Which alignments are used?
- Why Smith-Waterman?
- Do we have a place to put data/code set up yet?
- Sample size issue (posted on collectiveX)
- AMPHORA on Delong: mean number of sequences is only 2
- versus Sargasso Sea (1.2 million sequences)
- Future studies will have 50,000 sequences or more
- Could look at more genes (still won't change depth of coverage per gene)
- Different types of genes - they will have different profiles across the landscape
- Combine genes. How?
- Concatenated alignment of all 31 markers for fully sequenced genomes, then place reads on this "genome" tree
- Could try other data sets
- For presence/absence
- what resolution?
- AMPHORA on Delong: mean number of sequences is only 2