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'STRAP:multiple sequence alignments '
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Package charite.christo.strap

Interface Summary
AlignmentWriter  
ProteinProteinDistance  
ProteinProteinSimilarity Returns high values for pairs of similar proteins and small values for dissimilar proteins.
ProteinProteinValue Returns values for pairs of proteins.
ProteinsSorter It can reorder proteins so that similar sequences are in adjacent lines.
StrapExtension StrapExtension defines a general multi-purpose plugin.
ValueOfAlignPosition Plugins that return a numeric value for each position (column) in the alignment or null.
 

Class Summary
AbstractAlignAndCompare  
AbstractAligner  
AbstractAlignerProxy  
AbstractAlignmentProject  
AbstractDialogJPanel  
AbstractDialogJTabbedPane  
AbstractDialogPredict The user can predict secondary structure or TM helices in selected proteins.
AcceptAlignment2  
ActivateDeactivate HELP With this form the text entries in residue annotations can be activated or deactivated or deleted.
AddAnnotation HELP With this form annotations can be added to residue annotations.
Aligner3D HELP Combining sequence alignment methods and 3D-superposition.
ComboKeys Choice menu for keys of residue selections.
ContextObjects  
CsaWeb  
Dialog_bl2seq HELP BL2SEQ produces all local alignments of two given sequences (UBIC:bl2seq).
Dialog3DViewer HELP PACKAGE:charite.christo.strap.extensions.
CLASS_REF:ChJmolPROXYJMOL CLASS_REF:PymolPYMOL CLASS_REF:ChAstexPROXYOpenAstex Installed by STRAP allways Linux Linux, Windows, Mac always Operation system all X-Windows all all Performance medium high high with accelerated video cards high Memory consumption high low medium medium # models per view many 1 many many Shows superimposed proteins yes no yes yes
Protein PDB structure viewers are used for detailed 3D-visualization.
Comparing different 3D-viewers
DialogAlign HELP The Dialog is used to align a number of selected proteins (see WIKI:Sequence_alignment).
DialogAlignOneToAll HELP With this dialog a reference protein can be aligned to many other proteins producing a pair-alignments for each protein.
DialogAlignOneToAllResult HELP
DialogAlignResult  
DialogBarChart HELP The bar chart visualizes values assigned to single proteins.
DialogBlast HELP STRAP allows to search public and private sequence databases to identify sequences that are similar to a query sequences.
DialogCompareProteins HELP This dialog allows the pairwise comparison of a set of proteins.
DialogCopyAnnotations HELP Residue annotations of one protein can be copied to the equivalent positions in another aligned protein.
DialogDifferentResidues HELP Based on the current sequence alignment two aligned proteins are compared residue by residue and all different residues are collected in a table.
DialogDotPlot HELP A dot-plot is a correlogram of two sequence WIKI:Dot_plot_(bioinformatics).
DialogDotPlot_Sequence  
DialogExportAlignment HELP The sequence alignment can be exported in various formats: HTML WIKI:Fasta_format HSSP-format is not frequently used: http://www.predictprotein.org/Dexa/out_hssp.html MSF-format: http://bmerc-www.bu.edu/examples/output/seqlist.msf.html ClustalW-format: http://www.molecularevolution.org/mbl/resources/fileformats/ SEE_DIALOG:Texshade SEE_DIALOG:DialogImportMFA SEE_DIALOG:DialogExportProteins
DialogExportProteins HELP
DialogExportWord  
DialogFetchPdb HELP This dialog aims at loading many PDB-files from file servers.
DialogFetchSRS HELP With this dialog a number of sequence files can be loaded from public servers.
DialogGenbank HELP 
   1    AAACATGGCG CTGGCTAGCG TGTTGCAGCG ...
DialogHighlightPattern HELP This dialog is used to underline all occurrences of sequence patterns.
DialogImportMFA HELP Multiple sequence files (WIKI:FASTA_format, MSF, BIOWIKI:NexusFormat, WIKI:Stockholm_format ) can be directly dragged into the alignment panel.
DialogInferCDS HELP With this Dialog one or more nucleotide sequences can be translated to amino acids according to the WIKI:Genetic_code.
DialogManyInOneRow HELP For manipulating several proteins simultaneously, more than one protein may be stacked in one single line by pressing either button: JCOMPONENT:DialogManyInOneRow#getButton("A")! or
JCOMPONENT:DialogManyInOneRow#getButton("X")! Only one representative is shown and the others are hidden.
DialogNeighbors HELP PACKAGE:charite.christo.strap.
DialogNeighborsResult  
DialogNewProtein HELP The user enters the name of a protein and an amino acid sequence.
DialogNonRedundantSequenceSet HELP A set of proteins is generated from the selected proteins
where the sequence identity ratio is not higher than the given threshold.

Proteins are excluded from the set for which another very similar protein exists.
This procedure is rather primitive and more sophisticated programs for this task exist (E.g.
DialogPhylogeneticTree HELP This dialog is used to draw phylogenetic dendrograms of aligned protein sequences.
DialogPlot HELP With this dialog numeric data is plotted along the sequence/alignment.
DialogPredictCoiledCoil HELP WIKI:Coiled_coil regions are predicted from amino acid sequences.
DialogPredictSecondaryStructures HELP WIKI:Secondary_structure are predicted from the amino acid sequences.
DialogPredictTexshade HELP Makes texshade commands for the structure prediction Text lines starting with a percent sign are ignored since "%" preceeds comments in WIKI:LaTeX.
DialogPredictTmHelices2 HELP At least one third of all proteins are transmembrane proteins but the 3D-structures of only a few are solved.
DialogPredictTmHelicesMulti  
DialogProteinList HELP A list of protein files is entered into the text area.
DialogPublishAlignment HELP
Figure: Generation of a Web link.
DialogRenameProteins  
DialogResidueAnnotationChanges HELP This dialog allows to perform string replacements in many annotations of residue selections at once.
DialogResidueAnnotationList HELP This dialog allows to create residue annotations from lists of the form 
E815R  G4711A  C4444Q
DialogRestoreFromBackup HELP A backup of the multiple sequence alignment data can be written to the directory "./backup/.
DialogSelectionOfResidues  
DialogSelectionOfResiduesMain HELP Residues selections are computed by a method chosen by the user.
DialogSimilarStructure HELP Only proteins that have 3D-coordinates, can be visualized in STRAP three-dimensionally.
DialogSimilarStructureResult  
DialogSortProteins HELP Proteins appear in the order they are loaded from HD.
DialogSubcellularLocalization HELP The cellular compartment is predicted from the amino acid sequence.
DialogSuperimpose3D HELP Two protein structures can be superimposed three-dimensionally using C-alpha coordinates so that they are oriented in 3D-space in the same way.
DialogSuperimpose3DResult  
Distance3DToCursor HELP In DIALOG:DialogSelectionOfResiduesMain the method COMBO:Distance3DToCursor is selected.
DnaExonStart HELP This operation creates residue selections at all beginnings of continuous blocks of translated nucleotides (WIKI:Exon, WIKI:Intron).
DrawGappedSequence A gapped sequence with colorshading is drawn.
EditDna HELP This Dialog allows to translate coding nucleotide sequences into amino acid sequences.
EditDnaTable  
ExpasyGff  
Export2Jalview HELP Jalview is an excellent well-known alignment viewer.
To name a few features: Evolutionary dendrograms Export of Encapsulated Postscript (eps) Images which can be included in OpenOffice documents. Jalview can retrieve and visualize features from many BioDAS* sources at once. When Jalview is started the first time ~9 Megabyte are downloaded.
ExportAlignment HELP

This alignment view has been generated with the sequence alignment program Strap.
FilesFetchedFromServer Common part of the dialogs DialogFetchSRS and DialogFetchPdb.
HeteroPopup  
HScrollBar The View of an alignment window has a horizontal scrollbar which is used as a viewport.
IntermediateSeq HELP Identifying Blast hits that are common to two sequences helps to compare remote homologs.
IntermediateSeqPair  
NextAndPrevSelection  
ProteinCombo A choice menu containing for selecting a protein.
ProteinComboModel A choice menu containing for selecting a protein.
ProteinList A JList to select proteins.
ProteinPopup The protein menu.
ProteinViewerPopup The menu for protein viewers (Pymol, Jmol ...
ResidueAnnotation HELP Residue annotations, allow the assignment of information to specific amino acids or nucleotides of proteins.
ResidueAnnotation.Entry  
ResidueAnnotationView HELP PACKAGE:charite.christo.strap.extensions. PACKAGE:charite.christo.protein. To edit a CLASS_REF:ResidueAnnotationresidue annotation The item BUTTON:ResidueSelectionPopup#ACTION_edit of the context menu must be activated.
ResidueSelectionPopup  
ResSelUtils  
SequenceFeatures HELP
SPUtils  
Strap HELP Each alignment project is stored in one file directory.
StrapAlign The root class of the alignment from which all information is accessible.
StrapDAS HELP BioDAS* services provide residue specific annotations for proteins.
StrapHotswap HELP The hotswap-dialog provides a comfortable environment for writing plugins.
StrapKeyStroke HELP The keyboard is used to move the alignment cursor and to introduced/removed alignment gaps.
Arrow keys Cursor navigation CTRL arrow keys move to beginning or end ALT + arrow keysmove to next gap HOME First row END Last row SHIFT HOME First column SHIFT END Last column
Cursor Movements
PAGE-UP / PAGE-DOWNScroll up and down SHIFT PAGE-UP Scroll left
Movement of the view-port
DELETE Delete gap right from or under cursor BACKSPACE DELETE gap left from cursor CTRL DELETE Delete next gap right from the cursor CTRL BACKSPACE Delete next gap left from cursor CTRL SHIFT DELETE Delete entire white space under cursor CTRL SHIFT BACKSPACEDelete entire white space left from cursor
Deleting gaps
SPACE Insert gap under cursor INSERT Insert gaps until next residue in above row is reached.
Inserting gaps
StrapMacApplicationListener  
StrapPlugin  
StrapPlugins  
StrapScriptInterpreter  
StrapTree HELP Context menus in STRAP: The term WIKI:Context_menu is commonly used for menus which pop up when right clicking (right mouse button) an item in a graphical user interface, offering a list of options which vary depending on the item selected.
StrapUtils  
StrapView HELP The central view of the STRAP application is the alignment panel.
Texshade  
TexshadeGraph  
Tutorials  
V3dListModel  
V3dUtils HELP

Menu-bar: If the user clicks inside the 3D-view, the default Strap menu-bar disappears and the menu-bar of the 3D-view is shown instead.
 

Overview   Package  Class  Tree  Deprecated  Index  Help 
'STRAP:multiple sequence alignments '
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'The most important classes are StrapAlign, Protein and StrapEvent.'