(1) contigs ordered by protein-level mapping to Lens genome:

(a) as multiple fasta:

454LargeContigs.fna_Lens_NC_006369.fna.proteinmatch.orderedcontigs.mfasta

(b) and as single fasta sequence:

454LargeContigs.fna_Lens_NC_006369.fna.proteinmatch.orderedcontigs.fasta


(2) ordered contigs crunched against 4 Legionella genomes:

454LargeContigs.fna_orderedByProteinMatchLens_Lens.crunch
454LargeContigs.fna_orderedByProteinMatchLens_Philadelphia1.crunch
454LargeContigs.fna_orderedByProteinMatchLens_Corby.crunch
454LargeContigs.fna_orderedByProteinMatchLens_Paris.crunch


(3) to view these in ACT:
act 454LargeContigs.fna_Lens_NC_006369.fna.contigs.mfasta 454LargeContigs.fna_orderedByProteinMatchLens_Lens.crunch Lens_NC_006369.gbk
act 454LargeContigs.fna_Lens_NC_006369.fna.contigs.mfasta 454LargeContigs.fna_orderedByProteinMatchLens_Philadelphia1.crunch Philadephia1_NC_002942.gbk
act 454LargeContigs.fna_Lens_NC_006369.fna.contigs.mfasta 454LargeContigs.fna_orderedByProteinMatchLens_Corby.crunch Corby_NC_009494.gbk
act 454LargeContigs.fna_Lens_NC_006369.fna.contigs.mfasta 454LargeContigs.fna_orderedByProteinMatchLens_Paris.crunch Paris_NC_006368.gbk


(4) Unmapped sequences

(a) 454 contigs that couldn't be mapped to Lens at the protein level:

454LargeContigs.fna_Lens_NC_006369.fna.proteinmatch.NOTMAPPEDTOLENS.fasta

(b) Regions of Lens genome that weren't covered by 454 contigs:

proteinmatch.Lens_NC_006369.NOTCOVEREDBY454.fasta


(5) Preliminary SNP calls 
- using MUMmer/nucmer, with default settings, no filtering
- these should be treated warily as they will contain errors due to 
  -- mismapping in repetitive regions
  -- proximity to contig ends
  -- proximity to homopolymeric tracts which are problematic for 454
  -- low quality base calls
- note the positions (col1) for SNP loci in each file pertain to the different reference sequence, so can't be directly compared
  -- to draw a tree based on SNPs, I would map each of the other 3 genomes to Lens (as the reference) and compare SNPs relative to Lens
  -- it would be better to attempt a whole-genome tree, using e.g. Mauve
lens.snps
philadelphia1.snps
corby.snps
paris.snps