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List of Figures

  1. Simplified shotgun sequencing process
  2. Amplification of DNA through vectors
  3. Location of forward and reverse reads on plasmids
  4. Example for trace data with the four gel lanes superposed.
  5. Example for bad trace signal quality, start of trace
  6. Example for good trace signal quality, middle of trace
  7. Example for bad signal quality, end of a trace
  8. Example for a gene architecture in eukaryotic genomes.
  9. Example for gene splice variations in eukaryotic genomes.
  10. Conventional assembly
  11. Integrated assembly
  12. Explainable assembly discrepancy
  13. Unexplainable assembly discrepancy
  14. Phases of a MIRA assembly cycle
  15. Mode of operation for DNASAND
  16. Transforming a nucleotide 8-tuple (octet) into a 16 bit hash.
  17. Transforming an octet with an undefined base into hashes
  18. Computation of the combined hash-position table
  19. Splitting a combined hash-position table into subtables.
  20. Computing a octet distance histogram.
  21. Compressing imprints into boolean arrays.
  22. Transforming 9-tuples into hashes allowing for errors
  23. Read scan matrices.
  24. Smith-Waterman banding.
  25. Smith-Waterman band prediction
  26. Smith-Waterman (SW) band calculation predecessor rules
  27. Modified Smith-Waterman algorithm: accepted match.
  28. Modified Smith-Waterman algorithm: rejected match.
  29. Assembly overlap graph.
  30. Example for an assembly graph
  31. Path building examples.
  32. Assembly graph example.
  33. Failure example when using simple read acceptance strategies in contigs.
  34. Contig using additional sequencing information.
  35. Example for using strict signal checking in contig standard repeat regions.
  36. Calculating base group qualities
  37. Discovery of previously unknown long term repeats.
  38. Resolved long term repeats with PRMB tags.
  39. Extension of confidence regions.
  40. Coverage example in non-normalised EST project
  41. Detection of SNP base in EST sequences
  42. Merging mRNA transcripts
  43. Categorising SNPs with sequences that have strain information
  44. Sample of an assembly HTML output

Bastien Chevreux 2006-05-11