14.12.2007

meeting at 14.12.07

design of a new data format to store population genetics data:
- XML or XML like
- not to complex that you can have a look on your data in the text format
- e.g.:
  - header: Name, Population, number of loci, history of loci (IDs), (loci information), no of individuals/sequences, interleaved data,…
  - data: in a table like form with IDs, Frequency, Data (<ID>…</ID> <Freq>…</Freq> <Genot>…</Genot>)
also look at different databases/formats:
- ENSEMBL (in FASTA format)
- HapMap: HapMap:ENCODE Data
- HGDP
- ENCODE (resequencing HapMap)
- A Prototype Object Database for Mitochondrial DNA Variation -- Neigel and Leberg 95 (1): 85 -- Journal of Heredity
- TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks -- Heida et al. 20 (Supplement 1): i152 -- Bioinformatics
- The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet
- SOLEXA: information on how solexa data are handled and concatenated
- FASTA (It seems also that the FASTA format is pretty well spread and it would be worth having a look at)

R-lequin:
- give information about how to structure and set XML tags in the output of Arlequin (good visualisation and data extraction to make graphics)
- to do until January

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