-
Notifications
You must be signed in to change notification settings - Fork 16
Expand file tree
/
Copy pathBioJava:CookBook4.0.html
More file actions
201 lines (160 loc) · 8.57 KB
/
BioJava:CookBook4.0.html
File metadata and controls
201 lines (160 loc) · 8.57 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
<h2 id="biojava-cookbook-for-release-4">BioJava Cookbook for release 4.*</h2>
<p>BioJava 3+ is a major re-write of BioJava 1. As such many things work
differently. This cookbook provides examples how to work with the new
codebase.</p>
<p>The page was inspired by various programming cookbooks and follows a
“How do I…?” type approach. Each “How do I?” is linked to some example
code that does what you want and sometimes more. Basically if you find
the code you want and copy and paste it into your program you should be
up and running quickly. I have endeavoured to over document the code to
make it more obvious what I am doing so some of the code might look a
bit bloated.</p>
<p>If you have any suggestions, questions or comments contact the <a href="mailto:biojava-l@biojava.org">biojava
mailing list</a>. To subscribe to this list
go <a href="http://biojava.org/mailman/listinfo/biojava-l">here</a></p>
<p><strong>Please cite:</strong></p>
<h2 id="tutorial">Tutorial</h2>
<p>Many topics are also covered in the <a href="https://github.com/biojava/biojava-tutorial">BioJava
tutorial</a>.</p>
<h2 id="how-do-i">How Do I….?</h2>
<h3 id="core-module---working-with-sequences">Core Module - Working with Sequences</h3>
<p><strong>Required modules</strong>: <em>biojava-core</em></p>
<ul>
<li><a href="BioJava:CookBook:Core:Overview" title="wikilink">Overview of
biojava-core?</a></li>
<li><a href="BioJava:CookBook:Core:Sequences" title="wikilink">How are sequences
created?</a></li>
<li><a href="BioJava:CookBook:Core:SequenceCompare" title="wikilink">How do I compare two DNA Sequences and create a consensus
sequence?</a></li>
<li><a href="BioJava:CookBook:Core:FastaReadWrite" title="wikilink">How do I read or write Fasta
files?</a></li>
<li><a href="BioJava:CookBook:Core:GenbankRead" title="wikilink">How do I read Genbank
files?</a></li>
<li><a href="BioJava:CookBook:Core:SequenceFeaturePanel" title="wikilink">How do I view Features on a
sequence?</a></li>
</ul>
<h3 id="protein-structure">Protein Structure</h3>
<p><strong>Required modules</strong>: <em>biojava-structure, biojava-alignment</em> <strong>Optional
module</strong> : <em>biojava-structure-gui</em> for the 3D visualisation <strong>Optional
external library</strong> : <em>JmolApplet.jar</em> for the 3D visualisation</p>
<ul>
<li><a href="BioJava:CookBook:PDB:read3.0" title="wikilink">How can I parse a PDB
file?</a></li>
<li><a href="BioJava:CookBook:PDB:mmcif" title="wikilink">How can I parse a .mmcif
file?</a></li>
<li><a href="BioJava:CookBook:PDB:datamodel" title="wikilink">What is the BioJava structure
datamodel?</a></li>
<li><a href="BioJava:CookBook:PDB:atomsCalc" title="wikilink">How can I do calculations on
atoms?</a></li>
<li><a href="BioJava:CookBook:PDB:header" title="wikilink">How can I access the header information of a PDB
file?</a></li>
<li><a href="BioJava:CookBook:PDB:seqres" title="wikilink">How does BioJava deal with SEQRES and ATOM
groups?</a></li>
<li><a href="BioJava:CookBook:PDB:mutate" title="wikilink">How can I mutate a
residue?</a></li>
<li><a href="BioJava:CookBook:PDB:align" title="wikilink">How can I calculate a structure
alignment?</a></li>
<li><a href="BioJava:CookBook:PDB:alignGUI" title="wikilink">How can I use a simple GUI to calculate an
alignment?</a></li>
<li><a href="BioJava:CookBook:PDB:Jmol" title="wikilink">How can I interact with
Jmol?</a></li>
<li><a href="BioJava:CookBook:PDB:hibernate" title="wikilink">How can I serialize to a
database?</a></li>
<li><a href="BioJava:CookBook:PDB:SCOP" title="wikilink">How can I load data from the SCOP
classification?</a></li>
<li><a href="BioJava:CookBook:PDBP:BerkeleySCOP" title="wikilink">How can I work with the Berkeley version of
SCOP?</a></li>
<li><a href="BioJava:CookBook:PDB:ligands" title="wikilink">How can I find residues binding a
ligand?</a></li>
<li><a href="BioJava:CookBook:PDB:bioassembly" title="wikilink">How to work with biological assemblies of
proteins</a></li>
<li><a href="BioJava:CookBook:PDB:restful" title="wikilink">How to get information using RCSB’s RESTful
services</a></li>
<li><a href="BioJava:CookBook:PDB:restful" title="wikilink">How do I calculate the true length of a
structure?</a></li>
</ul>
<h3 id="pairwise-and-multiple-sequence-alignment">Pairwise and Multiple Sequence Alignment</h3>
<p><strong>Required modules</strong>: <em>biojava-alignment, biojava-core, biojava-phylo</em>
<strong>Required external library</strong>: <em>forester.jar</em></p>
<ul>
<li><a href="BioJava:CookBook3:Stockholm" title="wikilink">How can I read a Sequence Alignment in Stockholm
format</a>? (Pfam, Rfam)</li>
<li><a href="BioJava:CookBook3:PSA" title="wikilink">How can I calculate a Pairwise Sequence
Alignment</a>? (Smith Waterman,
Needleman Wunsch)</li>
<li><a href="BioJava:CookBook3:PSA_DNA" title="wikilink">How can I calculate a Pairwise Sequence Alignment with DNA
sequences</a>?</li>
<li><a href="BioJava:CookBook3:MSA" title="wikilink">How can I create a Multiple Sequence
Alignment</a>?</li>
<li><a href="BioJava:CookBook3:MSAProfiler" title="wikilink">How can I profile the time and memory requirements of a Multiple
Sequence Alignment</a>?</li>
</ul>
<h3 id="genome">Genome</h3>
<p><strong>Required modules</strong>: <em>biojava-genome</em></p>
<ul>
<li><a href="BioJava:CookBook:genome:Overview" title="wikilink">Overview of
biojava-genome?</a></li>
</ul>
<h3 id="sequencing">Sequencing</h3>
<p><strong>Required modules</strong>: <em>biojava-core</em>,<em>biojava-sequencing</em> <strong>Required
external library</strong>: <em>guava-11.0.1.jar</em></p>
<ul>
<li><a href="Biojava:CookBook3:FASTQ" title="wikilink">How do I work with nextgen sequencing reads in FASTQ
format?</a></li>
</ul>
<h3 id="phylogenetic-tree">Phylogenetic tree</h3>
<p><strong>Required modules</strong>: ‘‘biojava-core <strong>Required external library</strong>:
<em>forester.jar</em></p>
<ul>
<li><a href="BioJava:CookBook:Phylo:Overview" title="wikilink">Overview of
biojava-phylo?</a></li>
</ul>
<!-- -->
<ul>
<li><a href="BioJava:CookBook:Phylo:ProfileToMSA" title="wikilink">How do I convert Profile object into Multiple Sequence Alignment
object to be use in the
TreeConstructor</a></li>
</ul>
<h3 id="physico-chemical-properties-computation">Physico-Chemical Properties Computation</h3>
<p><strong>Required modules</strong>: <em>biojava-aa-prop, biojava-structure and
biojava-core</em></p>
<ul>
<li><a href="BioJava:CookBook:AAPROP:main" title="wikilink">How can I compute physico-chemical properties via
APIs?</a></li>
<li><a href="BioJava:CookBook:AAPROP:commandprompt" title="wikilink">How can I compute physico-chemical properties using Command
Prompt?</a></li>
<li><a href="BioJava:CookBook:AAPROP:profeat" title="wikilink">How can I compute PROFEAT properties via
APIs?</a></li>
</ul>
<h3 id="protein-disorder">Protein Disorder</h3>
<p><strong>Required modules</strong>: <em>biojava-protein-disorder</em></p>
<ul>
<li><a href="BioJava:CookBook3:ProteinDisorder" title="wikilink">How can I predict disordered regions of the protein using its
sequence?</a></li>
<li><a href="BioJava:CookBook3:ProteinDisorderCLI" title="wikilink">Can I use the predictor from the command
line?</a></li>
</ul>
<h3 id="protein-modification-identification">Protein Modification Identification</h3>
<p><strong>Required modules</strong>: <em>biojava-modfinder, biojava-structure</em></p>
<ul>
<li><a href="BioJava:CookBook3:ModFinder" title="wikilink">How can I identify protein modifications in a 3D
structure?</a></li>
<li><a href="BioJava:CookBook3:SupportedProtMod" title="wikilink">How can I get the list of supported protein
modifications?</a></li>
<li><a href="BioJava:CookBook3:AddProtMod" title="wikilink">How can I define and register a new protein
modification?</a></li>
</ul>
<h3 id="remote-web-service-calls">Remote Web Service Calls</h3>
<p><strong>Required modules</strong>: <em>biojava-core, biojava-ws</em></p>
<ul>
<li><a href="BioJava:CookBook3:NCBIQBlastService" title="wikilink">How can I use NCBI’s QBlast service
?</a></li>
<li><a href="BioJava:CookBook3:ParsingBlastXMLOutput" title="wikilink">How can I use Blast XML Output in my
program?</a></li>
<li><a href="BioJava:CookBook3:HmmerService" title="wikilink">How can I get Pfam annotations for a protein sequence using the
Hmmer3 service?</a></li>
</ul>
<h2 id="legacy-18x-cookbook">Legacy 1.8.x CookBook</h2>
<p>The CookBook for the legacy 1.8.x code base is available from</p>
<biojava:cookbooklegacy>.
</biojava:cookbooklegacy>