Package charite.christo.strap.extensions

Class Summary

AbstractSubcellularLocation
Aligner3D_Mapsci
Aligner3D_Matt
Aligner3D_Mustang	Authors: Arun S.
Aligner3D_Smolign	Author: Ivaylo Ilinkin and Ravi Janardan Publication: PUBMED:20122279
AlignmentEntropy	HELP A profile of the sequence variability of the multiple sequence alignment is displayed.
AlignmentScore
AlignmentWriterHSSP	HELP Example ## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics NR.
CoiledCoil_PredictorRobinson
ConsensusSequence	HELP All identical residues of aligned protein sequences are determined.
CountResidues	HELP This class counts the amino acids in a protein.
DemoAssociateObjectsToProteins	HELP This demo shows how own objects can be attached, retrieved and removed from proteins.
Distance3DToHetero	HELP A white space separated list of hetero-groups is needed.
Hydrophobicity	HELP This was translated from HydrophobicityProfiler.pl into java at http://gchelpdesk.ualberta.ca/servers/HydrophobicityProfiler/HydrophobicityProfiler.php See MOL_TOOLKIT:hydropathy Related links: Description of hydrophobicity scales: http://www.clcbio.com/index.php?id=43
IndividualSequenceDisSimilarity
MultipleAligner_SPEM	HELP SPEM aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment.
MultipleAlignerAlign_m	HELP Align-m is an accurate and highly versatile multiple alignment program.
MultipleAlignerAmap	HELP Author: A.S.
MultipleAlignerClustalW	HELP ClustalW is a widely applied program to generate multiple sequence alignments automatically.
MultipleAlignerDialign	HELP Home-page http://dialign.gobics.de/ Author: Burkhard Morgenstern and Said Abdeddaim Publication: PUBMED:10222408
MultipleAlignerDialignT	HELP Home: HOME_PAGE:MultipleAlignerDialignT Author: Amarendran R.
MultipleAlignerKalign	HELP Home page HOME_PAGE:MultipleAlignerKalign Author: Timo Lassmann Publication: PUBMED:16343337
MultipleAlignerMafft	HELP Mafft is an alignment program published in PUBMED:15661851
MultipleAlignerMuscle	HELP HOME: HOME:MultipleAlignerMuscle Windows (cygwin): Building the program fails Publication: PUBMED:15318951 MS_Windows: To build the package successfully please change the file intmath.cpp: Move the definition of the method log2(double) to the top and rename it e.g.
MultipleAlignerProbcons2	HELP Author: Mahathi Mahabhashyam Publication: PUBMED:15687296
MultipleAlignerT_Coffee	HELP Publication: PUBMED:10964570 Author: Cedric Notredame
PairAlignerJAligner
PairAlignerJAlignerPROXY	HELP JAligner: Java-implementation of the Smith Waterman algorithm for local sequence alignments.
PairAlignerNeoBio
PairAlignerNeoBioPROXY	HELP Home: http://neobio.sourceforge.net/ Depending on the settings it produces local or global sequence alignments.
PhylogeneticTree_Archaeopteryx	HELP Archaeopteryx takes a multiple sequence alignment and displays a phylogenetic tree.
PhylogeneticTree_TreeTop	HELP Web: HOME_PAGE:PhylogeneticTree_TreeTop Publication: PUBMED:7578577
ProteinsSorter_with3D_without3D
ResidueHydrophobicity_TOPPRED	HELP Web site: HOME_PAGE:Toppred Publication: PUBMED:7704669 Authors: von Heijne, Claros, Deveaud and Schuerer SEE_CLASS:TransmembraneHelix_TOPPRED
ResidueSolventAccessibility	HELP The solvent accessibility of a protein is currently loaded only from dssp-files.
ResidueValues_from_textfile	HELP The purpose of this class is to assign numeric values to residues in proteins.
RmsdValue
SecondaryStructure_Jnet	Web: HOME_PAGE:SecondaryStructure_Jnet Author: James Cuff and Geoff Barton Publication: PUBMED:10861942 Download: http://www.compbio.dundee.ac.uk/~www-jpred/jnet/download.html The following modification was necessary for Windows: jnet.h "#define MAXSEQNUM 600" changed to "#define MAXSEQNUM 60";
SecondaryStructure_NNPREDICT	HELP Server: HOME_PAGE:SecondaryStructure_NNPREDICT Author: Donald Kneller, Server: Nomi Harris
SecondaryStructure_Sopma	HELP Authors: C Geourjon and G Deleage.
SequenceDisSimilarityAsAligned	HELP This class calculates the ratio of identical residues of two aligned proteins.
SubcellularLocationHum_mPloc	HELP http://chou.med.harvard.edu/bioinf/hum-multi/ Author:Hong-Bin Shen and Kuo-Chen Chou Publication PUBMED:17346678
SubcellularLocationPLOC	HELP http://www.genome.jp/SIT/plocdir/ Publication PUBMED:12967962 Author: Keun-Joon Park and Minoru Kanehisa (2003)
SubcellularLocationSherLoc	HELP Publication:: PUBMED:17392328 PUBMED:17094224
Superimpose_CE	HELP Publication: PUBMED:11125099 , PUBMED:9796821 This is the Java based implementation of CE/CL superposition.
Superimpose_CEPROXY	HELP CE/CL ported to Java by Andreas Prlic
Superimpose_GangstaPlus	HELP GangstaPlus* Authors: Aysam Guerler, Bjoern Kolbeck, Connie Wang, Patrick May, Thomas Steinke, Tobais Schmidt-Goenner, Group Leader: Ernst-Walter Knapp Publication: PUBMED:18583523 PUBMED:17118190
Superimpose_Goede
Superimpose_GoedePROXY	HELP The C-alpha positions of two proteins are superimposed.
Superimpose_LajollaProtein	HELP Depending on the settings it produces local or global sequence alignments.
Superimpose_LajollaProteinPROXY	HELP Home: http://lajolla.sf.net Written in Java by Raphael Bauer
Superimpose_LajollaRNA	HELP Home: http://lajolla.sf.net Written in Java by Raphael Bauer
Superimpose_native_CE	HELP Publication: PUBMED:11125099 , PUBMED:9796821
Superimpose_TM_align	HELP Publication: PUBMED:15849316 Home page: HOME_PAGE:Superimpose_TM_align Authors: Yang Zhang and Jeffrey Skolnick
Toppred
TransmembraneHelix_DAS	HELP Server site: HOME_PAGE:TransmembraneHelix_DAS Author: Miklos Cserzo
TransmembraneHelix_HMMTOP	HELP Web site: HOME_PAGE:TransmembraneHelix_HMMTOP Publication: PUBMED:11590105 Authors: G.E.
TransmembraneHelix_MEMSAT	HELP Web site: HOME_PAGE:TransmembraneHelix_MEMSAT Authors: David T.
TransmembraneHelix_ORIENTM	HELP Web site: HOME_PAGE:TransmembraneHelix_ORIENTM Publication: PUBMED:11477216 Authors: Theodore D.
TransmembraneHelix_Phobius	HELP Web site: HOME_PAGE:TransmembraneHelix_Phobius Publication: PUBMED:15111065 Author: Lukas Kall
TransmembraneHelix_PRED_TMR	HELP Home page: HOME_PAGE:TransmembraneHelix_PRED_TMR Author: Claude Pasquier
TransmembraneHelix_SOSUI	HELP Web site: HOME_PAGE:TransmembraneHelix_SOSUI Developed at Mitaku Group, Department of Biotechnology Tokyo University of Agriculture and Technology
TransmembraneHelix_SPLIT3	HELP Authors: Davor Juretic, Croatia.
TransmembraneHelix_SPLIT4	HELP INCLUDE_DOC:TransmembraneHelix_SPLIT3
TransmembraneHelix_THUMBUP	HELP Web site: HOME_PAGE:TransmembraneHelix_THUMBUP, Maintainer: Hongyi Zhou.
TransmembraneHelix_TMAP	HELP Server HOME_PAGE:TransmembraneHelix_TMAP Authors: B Persson and P Argos Publication: PUBMED:9246628
TransmembraneHelix_TMAP_MULTI	HELP Server: HOME_PAGE:TransmembraneHelix_TMAP_MULTI It takes a multiple sequence alignment as input and predicts the transmembrane helices from the alignment.
TransmembraneHelix_TMHMM2	HELP Server: HOME_PAGE:TransmembraneHelix_TMHMM2 Maintained by Anders Krogh and Kristoffer Rapacki
TransmembraneHelix_TMPRED	HELP Web site: HOME_PAGE:TransmembraneHelix_TMPRED Author: K Hofmann and W Stoffel
TransmembraneHelix_TOPPRED	HELP Web site: HOME_PAGE:Toppred", Publication: PUBMED:7704669 Authors: von Heijne, Claros, Deveaud and Schuerer SEE_CLASS:ResidueHydrophobicity_TOPPRED
TransmembraneHelix_WaveTM	HELP Home: HOME_PAGE:TransmembraneHelix_WaveTM Publication: PUBMED:15107018 Maintainer: Zoi Litou