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Merged
sbliven merged 22 commits into from
Jul 22, 2015
Merged

Extend structure alignment page with multiple alignments #5

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509057f
Adding basic alignmentcode page with MultipleStructureAlignment proposal
sbliven Jul 10, 2014
e60bfea
Explanation for AFPChain Data Model
lafita Jul 21, 2015
30a0202
Update references and section template
lafita Jul 21, 2015
f095f28
Explain MultipleAlignment object hierarchy
lafita Jul 21, 2015
ac15b5d
Include examples for the two data models
lafita Jul 21, 2015
fa0fae2
Change protein references to structure
lafita Jul 22, 2015
a45465c
Add figures for multiple GUI
lafita Jul 22, 2015
34a1a4d
Change multiple figures
lafita Jul 22, 2015
dd2b482
Describe the GUI for multiple alignments
lafita Jul 22, 2015
3e2f422
Update structure reference in README
lafita Jul 22, 2015
3118385
Update structure references in Structure modules
lafita Jul 22, 2015
9b6123b
Update first steps
lafita Jul 22, 2015
1990920
Update structure data model
lafita Jul 22, 2015
13b8380
Update caching
lafita Jul 22, 2015
ba593eb
Update chemcomp.md
lafita Jul 22, 2015
77fc195
Update mmCIF explanation
lafita Jul 22, 2015
bed1234
Update SEQRES
lafita Jul 22, 2015
b1b8204
Explain utility methods for MSTA manipulation
lafita Jul 22, 2015
b6b0a01
Description of the MultipleMC algorithm
lafita Jul 22, 2015
99c7cc2
Footer script compatible with python 2.6
lafita Jul 22, 2015
40b7c4d
Merge remote-tracking branch 'origin/multiplealignment' into multiple…
lafita Jul 22, 2015
bbc77f4
Update footers
lafita Jul 22, 2015
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Update references and section template
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@lafita
lafita committed Jul 21, 2015
commit 30a0202e3a6010ef730a57b75d99c1489f520356
6 changes: 5 additions & 1 deletion structure/alignment.md
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Expand Up @@ -158,6 +158,10 @@ Additional methods can be added by implementing the
[StructureAlignment](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/StructureAlignment.html)
interface.

## Multiple Structure Alignment

Since BioJava 4.1.0, multiple structure alignments can be generated.

## PDB-wide database searches

The Alignment GUI also provides functionality for PDB-wide structural searches.
Expand Down Expand Up @@ -249,7 +253,7 @@ file in various formats.

## See Also

For details about performing alignments programatically, see [Structure Alignment in BioJava](alignmentcode.md)
For details about the structure alignment data models in biojava, see [Structure Alignment Data Models](alignment-data-model.md)

## Acknowledgements

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