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Bio java
- 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?
- 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?
- 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?
- 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?
- 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?
- 53. How do I display Sequence coordinates?
- 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?
- 62. How can I access the atoms in a structure?
- 64. How to work with Groups (AminoAcid, Nucleotide, Hetatom)?
- 65. How can I access the header information of a PDB file?
- 68. How can I calculate a structure alignment?
- 69. How can I use a simple GUI to calculate an alignment?