ORDered ALignment Information Explorer
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Transcript of ORDered ALignment Information Explorer
![Page 1: ORDered ALignment Information Explorer](https://reader035.fdocuments.net/reader035/viewer/2022062422/56813552550346895d9cb225/html5/thumbnails/1.jpg)
ORDered ALignment Information Explorer
![Page 2: ORDered ALignment Information Explorer](https://reader035.fdocuments.net/reader035/viewer/2022062422/56813552550346895d9cb225/html5/thumbnails/2.jpg)
Alignment editor
Conservation computtion
“barcode” = schematic alignment
Phylogenic tree
3D viewer
=> sequence / structure / function / evolution cross-talks
Sequence Clustering
Features Editor
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AlignmentPositions
Taxa
Contexts
Exploring Alignment Information up to the residue Level
Globallevel
Clusteringslevel
SingleTaxaLevel
Full length
Domains
Motifs, secondary structures, …..
ResiduesX x x
3D structure
conservation
phylogeny
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Reads ALN, MSF, TFA, RSF, Macsims/XML, ORD file formats
What is an alignment ?- description of the alignment (NorMD score, date, etc …)- set of sequences
generic information (length, EC, phylogeny, …) features (PFAM-A, PROSITE, BLOCK, etc …)
- clustering = groups of sequences- conservation scores based on clustering
and Alignments :
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Sequence editing Clustering editing
CurrentAlignment
Overwrite current Create new MACSIM
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Ordalie parameters (colors, fonts, thresholds, …)
Description of the alignment (name, NorMD score, creation date, ...)
Original Set of aligned sequences- general information (length, pI, mol. Weight, …)- features (Pfam domain, secondary structures, …)- AA sequence
Coordinates of 3D structures corresponding to PDB entriesDescription of 3D objects (representation type, colors, etc …)
M 3 – new clusteringClustering 1Sequences set 1-> conservation
M 4 – edit sequencesClustering 1Edit Sequences-> conservation
M 5 – clust. + editClustering 2Edit Sequences-> conservation
Inside :
M 2 – macsims clusteringMacsims ClusteringOriginal Sequences set-> original conservation
M 1 – original alignmentOriginal Sequences set
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SQlite Database accessible through SQL statements ODBC compatible
Platform independantLight weight
Contains all Ordalie data preferences performances
ORD : file format
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Modes :- features- search- pairwise identity- sequences editor - features editor- clustering- trees- conservation- superposition
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Zone selection :•Whole alignment•By Feature•User defined
•Criterions :•% identity•pI•Length•Composition (aminoacid, physico-chemical groups)
•Clustering Methods :•Manual clustering by inserting/removing separators•Hierarchical classification + Secator•Kmeans + DPC•Mixture model + AIC
Clustering:
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Threshold Global Identity -> 100% IdentityGlobal Conserved -> >80% identity.Group Identity -> 100 % identity in group
Mean Distanceas cf ClustalX
Vector Normbased on a vectorial (polarity,volume) representation of amino acids
Liu2based on Blosum62
Entropytakes gaps and physico-chemical properties of AA intoaccount
Validity of score clustering ?
Conservation Methods :
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Key Usage Points :
Always leave a mode before entering a new one
Sequences selection : « à la Windows »- <Button-1> selects a sequence- <Control-Button-1> add current seq. to selection- <Shift-Button-1>
Zone selection :- All (button)- selecting a feature <Control-Button-1>- manuaally :
- <Button-1> for starting point- <Button-3> for ending point- <Shift-Button-3> to delete a selected zone
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TODO List :
Short term :- Bugs, if any …. ;-)- group naming- project handling- MacOS X version- documentation and tutorials- publication
Long term :- Bugs, if any …. ;-)- on-line web services- on-line Macsims calculation- on-line sequence, information, feature updating- 3D surface mapping of features.- ….
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Running Ordalie :
On surf/lameX :- setordalie- ordalie <filename>- ordalie <filename> option value option value
File formats: MSF, TFA, ALN, RSF, XML/Macsims and ORD
Conversion :ordalie toto.msf –convert ALN
- toto.aln
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