@@ -57,114 +57,115 @@ Busque informações no [Google
5757Scholar] ( http://scholar.google.com/scholar?q=biojava ) sobre publicações
5858a respeito do BioJava.
5959
60- How Do I ....?
61- -------------
60+ Como eu faço para ....?
61+ ----------------------
6262
63- ### Setup
63+ ### Instalação
6464
65- - [ Where do I get a Java
66- installation ] ( http://java.sun.com/downloads/ ) ?
67- - [ How do I get and install BioJava] ( BioJava:GetStarted " wikilink ") ?
65+ - [ Onde eu encontro a instalação do
66+ Java ] ( http://java.sun.com/downloads/ ) ?
67+ - [ Como obter a instalação do BioJava] ( BioJava:GetStarted " wikilink ") ?
6868
69- ### Alphabets and Symbols
69+ ### Alfabetos e Simbolos
7070
71- - [ How do I get a DNA, RNA or Protein
72- Alphabet ] ( Biojava:Cookbook :Alphabets " wikilink ") ?
71+ - [ Como obter o Alfabeto de DNA, RNA ou
72+ Proteina ] ( Biojava:CookbookPortuguese :Alphabets " wikilink ") ?
7373- [ How do I make a custom Alphabet from custom
74- Symbols] ( Biojava:Cookbook :Alphabets:Custom " wikilink ") ?
74+ Symbols] ( Biojava:CookbookPortuguese :Alphabets:Custom " wikilink ") ?
7575- [ How do I make a CrossProductAlphabet such as a codon
76- Alphabet] ( Biojava:Cookbook :Alphabets:CrossProduct " wikilink ") ?
76+ Alphabet] ( Biojava:CookbookPortuguese :Alphabets:CrossProduct " wikilink ") ?
7777- [ How do I break Symbols from CrossProduct Alphabets into their
78- component Symbols] ( Biojava:Cookbook:Alphabets:Component " wikilink ") ?
78+ component
79+ Symbols] ( Biojava:CookbookPortuguese:Alphabets:Component " wikilink ") ?
7980- [ How can I tell if two Alphabets or Symbols are
80- equal] ( Biojava:Cookbook :Alphabets:Cononical " wikilink ") ?
81+ equal] ( Biojava:CookbookPortuguese :Alphabets:Cononical " wikilink ") ?
8182- [ How can I make an ambiguous Symbol like Y or
82- R] ( Biojava:Cookbook :Alphabets:Ambiguous " wikilink ") ?
83+ R] ( Biojava:CookbookPortuguese :Alphabets:Ambiguous " wikilink ") ?
8384
8485### Basic Sequence Manipulation
8586
8687- [ How do I make a Sequence from a String or make a Sequence Object
87- back into a String] ( Biojava:Cookbook :Sequence " wikilink ") ?
88+ back into a String] ( Biojava:CookbookPortuguese :Sequence " wikilink ") ?
8889- [ How do I get a subsection of a
89- Sequence] ( Biojava:Cookbook :Sequence:SubSequence " wikilink ") ?
90+ Sequence] ( Biojava:CookbookPortuguese :Sequence:SubSequence " wikilink ") ?
9091- [ How do I transcribe a DNA Sequence to a RNA
91- Sequence] ( Biojava:Cookbook :Sequence:Transcribe " wikilink ") ?
92+ Sequence] ( Biojava:CookbookPortuguese :Sequence:Transcribe " wikilink ") ?
9293- [ How do I reverse complement a DNA or RNA
93- Sequence] ( Biojava:Cookbook :Sequence:Reverse " wikilink ") ?
94+ Sequence] ( Biojava:CookbookPortuguese :Sequence:Reverse " wikilink ") ?
9495- [ Sequences are immutable so how can I change it's
95- name] ( Biojava:Cookbook :Sequence:ChangeName " wikilink ") ?
96+ name] ( Biojava:CookbookPortuguese :Sequence:ChangeName " wikilink ") ?
9697- [ How can I edit a Sequence or
97- SymbolList] ( Biojava:Cookbook :Sequence:Edit " wikilink ") ?
98+ SymbolList] ( Biojava:CookbookPortuguese :Sequence:Edit " wikilink ") ?
9899- [ How can I make a sequence motif into a regular
99- expression] ( Biojava:Cookbook :Sequence:Regex " wikilink ") ?
100+ expression] ( Biojava:CookbookPortuguese :Sequence:Regex " wikilink ") ?
100101
101102### Translation
102103
103104- [ How do I translate a DNA or RNA Sequence or SymbolList to
104- Protein] ( Biojava:Cookbook :Translation " wikilink ") ?
105+ Protein] ( Biojava:CookbookPortuguese :Translation " wikilink ") ?
105106- [ How do I translate a single codon to a single amino
106- acid] ( Biojava:Cookbook :Translation:Single " wikilink ") ?
107+ acid] ( Biojava:CookbookPortuguese :Translation:Single " wikilink ") ?
107108- [ How do I use a non standard translation
108- table] ( Biojava:Cookbook :Translation:NonStandart " wikilink ") ?
109+ table] ( Biojava:CookbookPortuguese :Translation:NonStandart " wikilink ") ?
109110- [ How do I translate a nucleotide sequence in all six
110- frames] ( Biojava:Cookbook :Translation:SixFrames " wikilink ") ?
111+ frames] ( Biojava:CookbookPortuguese :Translation:SixFrames " wikilink ") ?
111112
112113### Proteomics
113114
114115- [ How do I calculate the mass and pI of a
115- peptide] ( Biojava:Cookbook :Proteomics " wikilink ") ?
116+ peptide] ( Biojava:CookbookPortuguese :Proteomics " wikilink ") ?
116117- [ How do I analyze the symbol properties of an amino acid sequence
117118 using the Amino Acid Index
118- database] ( Biojava:Cookbook :Proteomics:AAindex " wikilink ") ?
119+ database] ( Biojava:CookbookPortuguese :Proteomics:AAindex " wikilink ") ?
119120
120121### Sequence I/O
121122
122123- [ How do I write Sequences in Fasta
123- format] ( Biojava:Cookbook :SeqIO:WriteInFasta " wikilink ") ?
124+ format] ( Biojava:CookbookPortuguese :SeqIO:WriteInFasta " wikilink ") ?
124125- [ How do I read in a Fasta
125- file] ( Biojava:Cookbook :SeqIO:ReadFasta " wikilink ") ?
126+ file] ( Biojava:CookbookPortuguese :SeqIO:ReadFasta " wikilink ") ?
126127- [ How do I read a GenBank/EMBL/SwissProt
127- file] ( Biojava:Cookbook :SeqIO:ReadGES " wikilink ") ?
128+ file] ( Biojava:CookbookPortuguese :SeqIO:ReadGES " wikilink ") ?
128129- [ How do I extract GenBank/EMBL/Swissprot sequences and write them as
129- Fasta] ( Biojava:Cookbook :SeqIO:GBtoFasta " wikilink ") ?
130+ Fasta] ( Biojava:CookbookPortuguese :SeqIO:GBtoFasta " wikilink ") ?
130131- [ How do I turn an ABI sequence trace into a BioJava
131- Sequence] ( Biojava:Cookbook :SeqIO:ABItoSequence " wikilink ") ?
132+ Sequence] ( Biojava:CookbookPortuguese :SeqIO:ABItoSequence " wikilink ") ?
132133- [ How does sequence I/O work in
133- BioJava] ( Biojava:Cookbook :SeqIO:Echo " wikilink ") ?
134+ BioJava] ( Biojava:CookbookPortuguese :SeqIO:Echo " wikilink ") ?
134135
135136### Annotations
136137
137138- [ How do I list the Annotations in a
138- Sequence] ( BioJava:Cookbook :Annotations:List " wikilink ") ?
139+ Sequence] ( BioJava:CookbookPortuguese :Annotations:List " wikilink ") ?
139140- [ How do I filter a Sequences based on their species (or another
140141 Annotation
141- property)] ( BioJava:Cookbook :Annotations:Filter " wikilink ") ?
142+ property)] ( BioJava:CookbookPortuguese :Annotations:Filter " wikilink ") ?
142143
143144### Locations and Features
144145
145146- [ How do I specify a
146- PointLocation] ( BioJava:Cookbook :Locations:Point " wikilink ") ?
147+ PointLocation] ( BioJava:CookbookPortuguese :Locations:Point " wikilink ") ?
147148- [ How do I specify a
148- RangeLocation] ( BioJava:Cookbook :Locations:Range " wikilink ") ?
149+ RangeLocation] ( BioJava:CookbookPortuguese :Locations:Range " wikilink ") ?
149150- [ How do CircularLocations
150- work] ( BioJava:Cookbook :Locations:Circular " wikilink ") ?
151+ work] ( BioJava:CookbookPortuguese :Locations:Circular " wikilink ") ?
151152- [ How can I make a
152- Feature] ( BioJava:Cookbook :Locations:Feature " wikilink ") ?
153+ Feature] ( BioJava:CookbookPortuguese :Locations:Feature " wikilink ") ?
153154- [ How can I filter Features by
154- type] ( BioJava:Cookbook :Locations:Filter " wikilink ") ?
155+ type] ( BioJava:CookbookPortuguese :Locations:Filter " wikilink ") ?
155156- [ How can I remove
156- features] ( BioJava:Cookbook :Locations:Remove " wikilink ") ?
157+ features] ( BioJava:CookbookPortuguese :Locations:Remove " wikilink ") ?
157158
158159### BLAST and FASTA
159160
160161- [ How do I set up a BLAST
161- parser] ( BioJava:CookBook :Blast:Parser " wikilink ") ?
162+ parser] ( BioJava:CookbookPortuguese :Blast:Parser " wikilink ") ?
162163- [ How do I set up a FASTA
163- parser] ( BioJava:CookBook :Fasta:Parser " wikilink ") ?
164+ parser] ( BioJava:CookbookPortuguese :Fasta:Parser " wikilink ") ?
164165- [ How do I extract information from parsed
165- results] ( BioJava:CookBook :Blast:Extract " wikilink ") ?
166+ results] ( BioJava:CookbookPortuguese :Blast:Extract " wikilink ") ?
166167- [ How do I parse a large file; Or, How do I make a custom
167- SearchContentHandler] ( BioJava:CookBook :Blast:Echo " wikilink ") ?
168+ SearchContentHandler] ( BioJava:CookbookPortuguese :Blast:Echo " wikilink ") ?
168169- Expert information on the BioJava SAX2 event based parsing framework
169170 by Cambridge Antibody Technology. Contains a UML diagram. Warning,
170171 this information may be a little dated now. (to be
@@ -174,79 +175,80 @@ How Do I....?
174175### Counts and Distributions
175176
176177- [ How do I count the residues in a
177- Sequence] ( BioJava:CookBook :Count:Residues " wikilink ") ?
178+ Sequence] ( BioJava:CookbookPortuguese :Count:Residues " wikilink ") ?
178179- [ How do I calculate the frequency of a Symbol in a
179- Sequence] ( BioJava:CookBook :Count:Frequency " wikilink ") ?
180+ Sequence] ( BioJava:CookbookPortuguese :Count:Frequency " wikilink ") ?
180181- [ How can I turn a Count into a
181- Distribution] ( BioJava:CookBook :Count:ToDistrib " wikilink ") ?
182+ Distribution] ( BioJava:CookbookPortuguese :Count:ToDistrib " wikilink ") ?
182183- [ How can I generate a random sequence from a
183- Distribution] ( BioJava:CookBook :Distribution:RandomSeqs " wikilink ") ?
184+ Distribution] ( BioJava:CookbookPortuguese :Distribution:RandomSeqs " wikilink ") ?
184185- [ How can I find the amount of information or entropy in a
185- Distribution] ( BioJava:CookBook :Distribution:Entropy " wikilink ") ?
186+ Distribution] ( BioJava:CookbookPortuguese :Distribution:Entropy " wikilink ") ?
186187- [ What is an easy way to tell if two Distributions have equal
187- weights] ( BioJava:CookBook :Distribution:Emission " wikilink ") ?
188+ weights] ( BioJava:CookbookPortuguese :Distribution:Emission " wikilink ") ?
188189- [ How can I make an OrderNDistribution over a custom
189- Alphabet] ( BioJava:CookBook :Distribution:Custom " wikilink ") ?
190+ Alphabet] ( BioJava:CookbookPortuguese :Distribution:Custom " wikilink ") ?
190191- [ How can I write a Distribution as
191- XML] ( BioJava:CookBook :Distribution:XML " wikilink ") ?
192+ XML] ( BioJava:CookbookPortuguese :Distribution:XML " wikilink ") ?
192193- [ Using Distributions to make a Gibbs
193- sampler] ( BioJava:CookBook :Distribution:Gibbs " wikilink ")
194+ sampler] ( BioJava:CookbookPortuguese :Distribution:Gibbs " wikilink ")
194195- [ Using Distributions to make a naive Bayes
195- classifier] ( BioJava:CookBook :Distribution:Bayes " wikilink ")
196+ classifier] ( BioJava:CookbookPortuguese :Distribution:Bayes " wikilink ")
196197- [ How do I calculate the composition of a Sequence or collection of
197- Sequences?] ( Biojava:CookBook :Distribution:Composition " wikilink ")
198+ Sequences?] ( Biojava:CookbookPortuguese :Distribution:Composition " wikilink ")
198199 This example uses JDK 1.5 and BioJavaX
199200
200201### Weight Matrices and Dynamic Programming
201202
202203- [ How do I use a WeightMatrix to find a
203- motif] ( BioJava:CookBook :DP:WeightMatrix " wikilink ") ?
204+ motif] ( BioJava:CookbookPortuguese :DP:WeightMatrix " wikilink ") ?
204205- [ How do I make a HMMER like profile
205- HMM] ( BioJava:CookBook :DP:HMM " wikilink ") ?
206+ HMM] ( BioJava:CookbookPortuguese :DP:HMM " wikilink ") ?
206207- |How do I set up a custom HMM? (Link to
207208 Tutorial?? --[ Guedes] ( User:Guedes " wikilink ") 11:43, 8 February 2006
208209 (EST) )
209210- [ How do I generate a pair-wise
210- alignment] ( BioJava:CookBook :DP:PairWise " wikilink ") with a Hidden
211- Markov Model?
211+ alignment] ( BioJava:CookbookPortuguese :DP:PairWise " wikilink ") with a
212+ Hidden Markov Model?
212213- [ How do I generate a global or local
213- alignment] ( BioJava:CookBook :DP:PairWise2 " wikilink ") with the
214- Needleman-Wunsch- or the Smith-Waterman-algorithm?
214+ alignment] ( BioJava:CookbookPortuguese :DP:PairWise2 " wikilink ") with
215+ the Needleman-Wunsch- or the Smith-Waterman-algorithm?
215216
216217### User Interfaces
217218
218219- [ How can I visualize Annotations and Features as a
219- tree] ( BioJava:CookBook :Interfaces:ViewAsTree " wikilink ") ?
220+ tree] ( BioJava:CookbookPortuguese :Interfaces:ViewAsTree " wikilink ") ?
220221- [ How can I display a Sequence in a
221- GUI] ( BioJava:CookBook :Interfaces:ViewInGUI " wikilink ") ?
222+ GUI] ( BioJava:CookbookPortuguese :Interfaces:ViewInGUI " wikilink ") ?
222223- [ How do I display Sequence
223- coordinates] ( BioJava:CookBook :Interfaces:Coordinates " wikilink ") ?
224+ coordinates] ( BioJava:CookbookPortuguese :Interfaces:Coordinates " wikilink ") ?
224225- [ How can I display
225- features] ( BioJava:CookBook :Interfaces:Features " wikilink ") ?
226+ features] ( BioJava:CookbookPortuguese :Interfaces:Features " wikilink ") ?
226227- [ How can I display Protein Features / a Peptide
227- Digest] ( BioJava:CookBook :Interfaces:ProteinPeptideFeatures " wikilink ") ?
228+ Digest] ( BioJava:CookbookPortuguese :Interfaces:ProteinPeptideFeatures " wikilink ") ?
228229
229230### BioSQL and Sequence Databases
230231
231232- [ How do I set up BioSQL with
232- PostgreSQL] ( BioJava:CookBook :BioSQL:SetupPostGre " wikilink ") ? (by
233- [ David Huen] ( User:David " wikilink ") )
233+ PostgreSQL] ( BioJava:CookbookPortuguese :BioSQL:SetupPostGre " wikilink ") ?
234+ (by [ David Huen] ( User:David " wikilink ") )
234235- [ How do I set up BioSQL with
235- Oracle] ( BioJava:CookBook :BioSQL:SetupOracle " wikilink ") ? (by
236- [ Richard Holland] ( User:Richard " wikilink ") )
236+ Oracle] ( BioJava:CookbookPortuguese :BioSQL:SetupOracle " wikilink ") ?
237+ (by [ Richard Holland] ( User:Richard " wikilink ") )
237238- [ How do I add, view and remove Sequence Objects from a BioSQL
238- DB] ( BioJava:CookBook :BioSQL:Manage " wikilink ") ?
239+ DB] ( BioJava:CookbookPortuguese :BioSQL:Manage " wikilink ") ?
239240
240241### Genetic Algorithms
241242
242243- [ How can I make a Genetic Algorithm with
243- BioJava] ( BioJava:CookBook :GA " wikilink ") ?
244+ BioJava] ( BioJava:CookbookPortuguese :GA " wikilink ") ?
244245
245246### Protein Structure
246247
247- - [ How can I read a PDB file?] ( BioJava:CookBook:PDB:read " wikilink ")
248+ - [ How can I read a PDB
249+ file?] ( BioJava:CookbookPortuguese:PDB:read " wikilink ")
248250- [ How can I mutate a
249- residue?] ( BioJava:CookBook :PDB:mutate " wikilink ")
251+ residue?] ( BioJava:CookbookPortuguese :PDB:mutate " wikilink ")
250252
251253### Protein Alignments and Secondary Structure Prediction with STRAP (by Christophe Gille)
252254
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