3. How do I make a custom Alphabet from custom Symbols?

4. How do I make a Cross Product Alphabet such as a codon Alphabet?

5. How do I break Symbols from Cross Product Alphabets into their component Symbols?

6. How can I tell if two Alphabets or Symbols are equal?

8. How do I get a subsection of a Sequence?

9. How do I transcribe a DNA Sequence to a RNA Sequence?

10. How do I reverse complement a DNA or RNA Sequence?

11. Sequences are immutable so how can I change it's name?

12. How can I edit a Sequence or Symbol List?

13. How can I make a sequence motif into a regular expression?

15. How do I translate a single codon to a single amino acid?

16. How do I use a non standard translation table?

17. How do I translate a nucleotide sequence in all six frames?

20. How do I read in a Fasta file?

21. How do I read a GenBank/EMBL/SwissProt file?(deprecated)

22. How do I read a GenBank/EMBL/UniProt/FASTA/INSDseq file?

23. How do I extract GenBank/EMBL/UniProt/FASTA/INSDseq sequences and write them as Fasta?

24. How do I turn an ABI sequence trace into a BioJava Sequence?

26. How do I extract Annotations for a set of Features?

28. How do I specify a RangeLocation?

29. How do CircularLocations work?

30. How can I make a Feature?

31. How can I filter Features by type?

33. How do I set up a FASTA parser?

34. How do I extract information from parsed results?

35. How do I parse a large file; Or, How do I make a custom SearchContentHandler?

37. How do I calculate the frequency of a Symbol in a Sequence?

38. How can I turn a Count into a Distribution?

39. How can I generate a random sequence from a Distribution?

40. How can I find the amount of information or entropy in a Distribution?

41. What is an easy way to tell if two Distributions have equal weights?

42. How can I make an OrderNDistribution over a custom Alphabet?

43. How can I write a Distribution as XML?

44. Using Distributions to make a Gibbs sampler

45. Using Distributions to make a naive Bayes classifier

47. How do I make a HMMER like profile HMM?

48. |How do I set up a custom HMM? (Link to Tutorial?? --Guedes 11:43, 8 February 2006 (EST) )

49. How do I generate a pair-wise alignment with a Hidden Markov Model?

51. How can I display a Sequence in a GUI?

52. How can I create a RichSequence viewer?

53. How do I display Sequence coordinates?

54. How can I display features?

55. How can I view an Alignment?

56. How can I view an Alignment II?

58. How do I set up BioSQL with Oracle? (by Richard Holland)

59. How do I add, view and remove Sequence Objects from a BioSQL DB?

61. How can I parse a .mmcif file?

62. How can I access the atoms in a structure?

63. How can I do calculations on atoms?

64. How to work with Groups (AminoAcid, Nucleotide, Hetatom)?

65. How can I access the header information of a PDB file?

66. How does BioJava deal with SEQRES and ATOM groups?

67. How can I mutate a residue?

68. How can I calculate a structure alignment?

69. How can I use a simple GUI to calculate an alignment?

70. How can I interact with Jmol?