Moore GreenLabNotesNov-21-08

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mtg notes

1. James will order new Mac Pro through Greg Soderstadt

2. Postpone reading Chivian et al paper

3. Steve will email OWW about deleting `members only' pages of the non-private iSEEM site. Mainly to avoid confusion about where to add new material. Also, why the sidebar on the private iSEEM site seems not to be working (e.g. quicknav etc) Plus can there be an auto-template for each page, which has menu bar at the top? TO save us doing this manually for each new page added.

4. Discussion of overlap between Pollard/Green lab on developing measures of diversity for use with metagenomic data. looking forward to further discussion at Davis

5. Discussion about Steve's AMPHORA workflow:

5.1 nucleotide vs peptide

(a) CAMERA data is nucleotide and so we need to convert to peptide sequences before using in AMPHORA (AMPHORA expects peptides). Need to use one of several possible programs to run through all six reading frames to pick out peptide sequence

(b) (program was suggested by Sourav on iSEEM phonecall, but we forget the name)

(c) CAMERA should hopefully be able to produce these peptide sequences for us, given their huge but thus far underused computing power

(d) does it make a difference (for a protein encoding gene) to construct a phylogeny using nucleotide or peptide sequences? What conceptually is the link?

Why does AMPHORA only use peptide sequences? Ask Martin and Jonathan why this is at next iSEEM phonecall