Jevtrace v3.12b User Manual Marcin Joachimiak 1/6/04
Contents
1. L M T Pap FER ao Figure 12 Displaying the average percent sequence identity for each node in the phylogenetic tree using the Annotate with ungapped sequence identity function in the Tree menu B jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln MYKSVETILVD IPTIRPHKLSVTIMOTOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL at IDTLLVDVPTVRPHKLSVATMNC QTL SVETILVDVPTIRPHRLSVATMNC OTL MIATPYKIESVETILVELPTIRPHRLSVATMNCOTL MIATPYKIESVETILVDVPTIRPHRLSVATMNCOTL MIPSAVQIQAVETILVDVPTIRPHRLSVATMNC ne MTALANPOILGIETILLDLPTIRPHVLAMATMHAQT MNAQITSVETVLVDLPTIRAHQLAMATMQOOTL MNAQITSVEA ILVDLPTIRAHOLAMATMOQO MHETNLEGEGMTAGMTATISSIEAILVDLPTIRAHOLAMATMOQO lt MEVATOOSITAIESIEAILVDLPTIRPHOLAMATMOROTI MIQAVIOSLESIIVDLPTIRPHKLAMHTMNROTI MSOAVIQSLESIIVDLPTIRPHKLAMHTMNRQ MSQVLIHSLSAIIVDLPTIRPHKLAMHTMQKQ MDTEMNRILIENLSAIIVDLPTIRPHKLAMHTMQNQ MTSALIERIEAIIVDLPTIRPHKLAMHTMQOQQ MTSALIERIDAIIVDLPTIRPHKLAMHTMQQO MSQVLIESVETIIVDLPTIRPHKLAMHTMQHQ MKIDAIEAVIVDVPTKRPIQMSITTVHQOSY MKIDAIDALIVDVPTRRP IOMSMTTVHOOS Y MKIEAIDVTLVDVPASRPIQMSFTTVQOKQSY MKIEAIDVTLVDVPASRPIOMSFTTVOKQOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY MRIESI AT IVDVPTRRPL km F TTVNKOS i Figure 13 Clicking on the ET button at the bottom of the Jevtrace window will c2. f MSA selections Undo last sequence selection reverts to the last sequence selections in the history Save sequence selections to file seqsel saves all the sequence selections to a text file in SeqSel format Load sequence selections from file seqsel reads sequence selections from a text file in SeqSel format Save coloring old versions of Chimera provided for backwards compatibility with older versions of chimera before August 2003 h Sequence Properties Mass Plot Volume Plot Electronegativity plot Hydrogen bond plot Entropy plot Oil water partition coefficient Kyte Doolittle hydrophobicity scale g MSA editing Undo last edit reverts to the sequences one step back in the history Insert gap adds a gap for every selection in the alignment Remove all gap columns removes all columns that are all gaps Remove character s removes any columns or characters selected in the alignment Remove selected column s Remove not selected column s Remove selected sequence s Remove not selected sequence s Cut columns left inclusive for a single selected column removes all columns to the left of the selection including the selection Cut columns right inclusive for a single selected column removes all columns to the right of the selection including the selection Export MSA graphics JPEG exports the alignment with colored selections to a JPEG file i Sequence
3. MSQVLIESVETIIVDLPTIRPHKLAMHTMOHQ MKIDAIEAVIVDVPTKRPIOMS ITTVHOOSY MKIDAIDALIVDVPTRRPIQMSMTTVHOOS Y MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKQSY MKIEAIDVTLVDVPASRPIQMSFTTVQOKQOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY MRIESITATIVDVP TERED TIVNKOS i Figure 2 Mouse clicking on any character will select that character or deselect if already selected 5 ad ay MLE_tcoffee aln nix 30 40 IIYKSVETILVDIPTIRPHKLSVTTMQTO HIDRIDTLLVDVPTVRPHKLSVATMNCQ MIATPVRIESVETILVDVPTIRPHRLSVATMNCO MIATPV SIESVETILVELPTIRPHRLSVATMNCOQ MIATPV SIESVETILVDVPTIRPHRLSVATMNCO MIPSAV IOAVETILVDVPTIRPHRLSVATMNCOA MNA ITSVETVLVDLPTIRAHQLAMATMQOQ MNA ITSVEAILVDLPTIRAHQLAMATMQOQ MHETNLHGKGMTAGMTABISSIEAILVDLPTIRAHOLAMATMQOO MKVATQOSIT IESIEAILVDLPTIRPHOLAMATMORQ MSQARIOSLES 1 IVDLPTIRPHKLAMHTMNRQ MSQARIOSLES 1 IVDLPTIRPHKLAMHTMNRQ MSQVIEIHSLSALIVDLPTIRPHKLAMHTMOKQ MD TEMNR IMIENLSAIIVDLPTIRPHKLAMHTMONO MTSAMIERIEAIIVDLPTIRPHKLAMHTMQOQ MTSAINIERIDAIIVDLPTIRPHKLAMHTMQOQ MSQVIBIESVETIIVDLPTIRPHKLAMHTMOHQ MSIDAIEAVIVDVPTKRPIQMSITTVHOOSY rere ew PERI mane FU KO CU TI ne ne ne T o MZIDAIDALIVDVPTRRPIQMSMTTVHQOSY MSIEAIDVTLVDVPASRPIQMSFTTVOKOSY MZSIEAIDVTLVDVPASRPIQMSFTTVOKOSY MSIEAIDVTLVDVPASRPIOMSFTTVOKOSY MBIEAIDVTLVDVPASRP IOMSFTTVOKOS MSIEAIDVTLVDVPASRPIOMSFTTVOKOSY Figure 3 Mouse clicking above any co
4. from Proteins Creighton 2 Edition hydrogen bonding potential counted as the total number of donor and acceptor groups entropy counted as the number of rotatable bonds the oil water partition coefficient kcal M per residue burial and the Kyte Doolittle hydrophobicity scale for transmembrane regions The relative value for each amino acid is shown by the green letters and orange lines The alternate blue and red coloring of positions is for contrast purposes only ES e java classes jevtrace 1g2r aln Volume Plot i Ol x Options 5 Making Multiple Alignments and Protein Structures Talk All structure viewing in Jevtrace is designated to the Java structure viewer WebMol Jevtrace and WebMol are distributed as an integrated package 5 1 Loading and associating a structure in Jevtrace To open a structure in Jevtrace the sequence of the structure has to be one of the sequences in the multiple alignment 1 Select the sequence in the alignment corresponding to the sequence of the structure Figure 4 The sequence should be identical in amino acids and length to the sequence of the PDB Discrepancies will be reported in a warning dialog window 2 Click the Open WebMol button at the bottom of the Jevtrace window A file dialog will prompt to choose a PDB format file 3 The PDB file will be read by Jevtrace and the sequence of the PDB structure will be aligned with the selected sequence in the alignment A warning dia
5. 6515 You will be emailed a download link for the jevtrace package For industrial licenses please contact Adelle Lohse The software will sent to the provided email account C Uncompress the Java package into a known directory D Depending on OS and preference proceed to setup or run Jevtrace The CLASSPATH modification allows for the easiest command line execution D 1 Alternately one can use a shortcut a script file such as a BAT bat file on Windows or setting the CLASSPATH through the command line cp option D 2 D 1 Add the directory from C to your system JAVA CLASSPATH For example on Windows set CLASSPATH c jevtrace_distr For details on setting the CLASSPATH for all OS please refer to the web Sun Microsystems provides details on setting the CLASSPATH for Windows Windows 95 and 98 Examine autoexec bat for the set command append Jevtrace directory to the set CLASSPATH line Other Windows NT Windows 2000 The CLASSPATH environment variable can be set using the System utility in the Control Panel AND OR D 2 If you do not feel like setting the CLASSPATH variable or you need to start right away you can use the cp option to start Java listing the relevant directories separated by a semicolon Simply type the following to start Jevtrace java cp c where is jevtrace package jevtrace jevtrace Note please do not add any other paths to the cp option 2 The Input Data A Multip
6. Names Name string search searches the sequence names with a query string selects matches Append unique number prefix appends an integer prefix to every name Strip numbers to make sequence names unique strips any existing integer sequence name prefix Convert names to species names extracts the species name and designates them as the new sequence names following the SwissProt convention e g LCA HUMAN or LCAA HORSE Export sequence names graphics JPEG exports the alignment with colored selections to a JPEG file j Tools Write sequence distances to file outputs the percent sequence identity for each unique pair of sequences to a tab delimited text file The file consists of the name of the first sequence name of second sequence and the percent sequence identity to two significant digits Write pairwise correlation data will generate a tab delimited text file encoding the pairwise sequence correlations based on the results graphically displayed on the alignment Currently only a binary 0 or 1 correlation scale is used and only residue pairs with non zero correlation data are output Export all graphics JPEG creates one JPEG graphic of the phylogenetic tree sequence names and sequence alignment k Colors Options in this menu allow selection of the active Jevtrace color Red and green are special colors It is important to pay attention to color conflicts when performing multiple nested
7. a single graphic MSA menu Export MSA graphics For example the following graphic shows columns colored by percent sequence identity using the color scale in section 4 1 and with columns containing gapped characters in green rit em HER HAMM HH HAMAHONA AMOH HMM eremi n nummum PH ret cin FUSE RTT TL EE te REAS TEAR AITAITA Ee HALLE BEEF DL LLL DUI THE miim e nne A rp CHERRY T tiebioes eis otii arista ede eres pest roben nr dor iopaap raidas ine enes en legere eot ertt poveri gn i E i H H i E B E E i eere Mildai idei dbrdapiabiebiddpi dhi doniada ri ado lar lic lanbra nido barro lnid E H B 5 E E 5 E H a 3 H H E HALUH SEE Eae ede bro Hae HELP LES These images are of high resolution such that any region can be zoomed in and viewed as legible characters MSN TS FEDVES METE YE RAGE LA LAA SHSISKSD MEYCHMIALLT ye MBA EC CSE TL Tig RESI CENE EFE Sole VO TENOR DVRS ENSEPHUAGUUYSHSVELEBNIBTEVSEEUGGTDEM TLE c SETE ME ROLES ADD Lee SL eee AE TAPP ART yy CRETA E r ESBRAUJTGUWG Er Er r IFEREVUESHNABEESABRUNM DOGS LGA ALFE a SES TENA TOA ATL LHe ee E UDERAD A LA L L Ta a 4 1 Selecting amino acids alignment columns and sequences Selections in the sequence alignment columns or individual characters or the sequence names are the basis for performing editing operations as well as mapping sequence information to protein
8. analysis e g color by percent identity then ET then correlation Color control brings up a dialog which allows control of which colors are displayed on the alignment and structure Use smooth color scale Jevtrace was originally designed with a discrete colored scale due to limitations in the structure graphics There is now the option to generate smooth scale coloring and this option allows to toggle translate between the two scales Coloring schemes Amino acid groups hydrophobic orange AFILMVWY hydrophilic NQST basic blue HKR acidic red DE cysteine yellow C proline magenta P glycine pink G Amino acid groups gaps hydrophobic orange AFILMVWY hydrophilic NQST basic blue HKR acidic red DE cysteine yellow C proline magenta P glycine pink G gaps black or or Phosphorylatable S T Y STY green Alignment quality Blosum62 BelVu style alignment quality coloring based on three similarity cutoffs l About About Lists the Jevtrace version and system settings
9. shown above the sequence alignment Clear Names Open WebMol requires a selected sequence in the alignment The sequence must be identical amino acids and length to the sequence of the structure User is prompted for a PDB file Jevtrace aligns the PDB sequence to the selected sequence If the alignment is successful displays the structure in WebMol This operation is required for any structure based computations Contacts requires an open protein structure For any selections in the MSA single seq or entire row computes residue residue contacts of those positions An all atom comparison is made using 6A as the contact cutoff Ligand contacts calculates the residues contacting the ligand if the PDB file has heteroatom records An all atom comparison is made using 6A asthe contact cutoff Clear MSA Clear All clears all selections in the MSA and tree canvases but not the Name canvas in order to avoid breaking and sequence PDB associations C Menus a File Open Tree and MSA open paired data consisting of tree and multiple sequence alignment A dialog first prompts for the tree file and then for the alignment Open MSA Open Tree Open Session File opens a saved session file and recreates any associated PDB sequence tree and name selections Save Session saves a session Quit quits the program b Tree Annotate with ungapped percent sequence identity annotates the tree with the percent sequen
10. ATISSIEAILYDLPTIRAHOLAMATMOOO corno ne re raro ron MKVATOOS ITAIES LEAILVDLPTIRPHOLAMATMOROQ I MSQAVIOSLESIIVDLPTIRPHKLAMHTMNRQ Pr n es rd nde rin MSOAVIOSLESIIVDLPTIRPHKLAMHTMNRO Mtn ne nt tt nna ne ne ne n e nt ne n nn MSQVLIHSLSAIIVDLPTIRPHKLAMHTMQKQ tente tarta MD TEMNRIL IENLSALIVDLPTIRPHKLAMHTMONO SAP MTSALIERIEAIIVDLPTIRPHKLAMHTMQOO MTSALIERIDAIIVDLPTIRPHKLAMHTMQOO MSQVLIESVETIIVDLPTIRPHKLAMHTMQHQ roer me me ma me a MKIDAIEAVIVDVPTKRPIQMSITTVHQQSY mann MKIDAIDALIVDVPTRRPIQMSMTTVHQOSY crono ve nero a noo MKIEAIDVTLVDVPASRPIQMSFTTVOKQSY Rann MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY e meme mo me no mo ve ne MKIEAIDVTLVDVPASRP IOMSFTIVOKOS Y d MKIEAIDVTLVDVPASRP IOMSFTTVOKOS Y d MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY tenerte nar na MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY me an me me reee MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY MRIESITATIVDVPTRRPLOMSFTTVNKOSY fl ee T P M EXT fae an 22 eal E Al gt J 4 B y E La zz US 5s US ss US PPP v MSD OKVESR DWP RPH A EOHI Saiyan et LiearDendrogram Create Parttions ET Coretatons Ovenwermol Contacts _ciearmsa ciesran r Figure 9 Using a mouse click while holding down the shift key will select all the subfamilies belonging to the originally selected node 6 2 Jevtrace analysis using selected subfamilies For example to analyze the evolutionary sequence correlations amongst the three subfa
11. ERIEAIIVDLPTIRPHKLAMHTMQQQ MTSALIERIDAIIVDLPTIRPHKLAMHTMQOQ MKIEAIDVILVDVPASRP IOMSFTTVOKOS Y MKIEAIDVILVDVPASRP IOMSFTTVOKOS Y MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY MRIESITATIVDVPTRRPLOMSFTTVNKOSY D OKVESRILDVPLIRPHGFA u Figure 8 Selection of subfamilies in the tree To select a subfamily of sequences click on the middle end of any branch Such selections are the basis for all advanced computations with Jevtrace including calculation of subfamily sequence conservation evolutionary correlations tracing the ancestors of a node and the Evolutionary Trace When the distances between sequences or ancestral nodes are small it can be difficult to see which sequences belong to a branch in this case click with the mouse while holding down the shift key This will select all the nodes below that node B jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln lolx 30 40 50 eee oe ne ne ne no ne ne me ne ne ne ne ne ae M MYKSVETILVDIPTIRPHKLSVTTMQTQ e me e me me me me me MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ tranne MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ rtt MIATPVKIESVETILVDVPTIRPHRLSVATMNCQ rtr MIATPVKIESVETILVELPTIRPHRLSVATMNCQ ttt mu EM Paha A AA A 7 Lal ifc apap alc afar n MNAQOITSVETVLVDLPTIRAHQLAMATMQQQ X M MNAQITSVEAILVDLPTIRAHQLAMATMQQQ 0000 ee 0 ttn MHETNLHGKGMTAGMT
12. GOIRLNORSL AP IMADES IESVEDAFSLAF RIRACQVLGDNGIDLIEQPISRINRGGOVRLNORSP APIMADESIESVEDAFSLAZ RIRACQVLGDNGIDLIEQPISRINRGGQVRLNORTP APIMADESIESVEDAFSLAZ RLRACRILGDNGIDLIEQPISRINRSGOVRLNORSP APIMADESIESVEDAFSLAZ RSVYIPELEALGVELIEQPVGRENTOALRRLSDNNR VAIMADESLSTLASAFDLAR RSIYIPELEALGVDLIEQPVARDNTRALRRLSETNR VAIMADESLSTLTSAFDLARE RSVWIPRLEAAGVELVEQPVARSNFDALRRLSADNG VAILADESLSSLASAFELAR ASVWIPRLEAAGVELVEOPVARSNFDALRRLSADNG VAILADESLSSLASAFELAR RSVWIPRLEAAGVELVEQOPVARSNFDALRRLSADNG VAILADESLSSLASAFELAR RSVWISRLEAAGVELVEQOPVARSNFDALRRLSADNG VAILADESLSSLASAFELAR RSVWIPRLEAAGVELVEQPVARSNFDALRRLSADNG VAILADESLSSLASAFELAR RSIWIPRLEEAGVELVEQPVPRANFGALRRLTEQNG VAILADESLSSLSSAFELAR ASIWIPRLEEAGVELVEQPVPRANFGALRRLTEQNG VAILADESLSSLSSAFELAR AS IBIPRREEAGVEBVEQENA puse eps fds eut aeons ds ELAH Figure 11 Creation of partitions of the phylogeny is enabled by clicking the Create Partitions button at the bottom of the Jevtrace window Once enabled clicking on the desired points in the phylogeny will produce a series of vertical colored lines Using the two functions in the Tree menu the partitions can be saved to or read from a file Write partitions from file will create a tab delimited text file with the relative position of each partition Read partitions from file will load this data and display it on the phylogenetic tree To aid in the selection of partitions the phylogenetic tree can be annotated with the average perc
13. Jevtrace v3 12b amp jevtrace dendogram c jevtrace_test MLE_tcoffee ph lt c jevtrace_test MLE_tcoffee aln 30 40 50 MYKSVETILVDIPTIRPHKLSVTTMQTOTI Meme MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ 7 MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ MIATPVKIESVETILVDVPTIRPHRLSVATMNCQTTI MIATPVKIESVETILVELPTIRPHRLSVATMNCOTL MIATPVKIESVETILVDVPTIRPHRLSVATMNC OTL MIPSAVQIQAVETILVDVPTIRPHRLSVATMNC ne MTALANPOILGIETILLDLPTIRPHVLAMATMHAQT MNAOITSVETVLVDLPTIRAHQLAMATMQQQTI MNAQITSVEAILVDLPTIRAHQLAMATMQOOTL MHETNLHGKGMTAGMTATISS IEAILVDLPTIRAHQLAMATMQQQ MKVATOOS ITAIES IEA ILVDLPTIRPHOLAMATMORO ee MIQAVIOSLESIIVDLPTIRPHKLAMHTMNRO MSOAVIOSLESIIVDLPTIRPHKLAMHTMNROTI MSOVLIHSLSAIIVDLPTIRPHKLAMHTMQKQTT MDTEMNRILIENLSAIIVDLPTIRPHKLAMHTMOQNQ MTSALIERIEAIIVDLPTIRPHKLAMHTMQQQ MTSALIERIDAIIVDLPTIRPHKLAMHTMQQQ MSOVLIESVETIIVDLPTIRPHKLAMHTMOHQ MKIDAIEAVIVDVPTKRPIQMSITTVHQOSY MKIDAIDALIVDVPTRRPIQMSMTTYHQOSY MKIEAIDVTLVDVPASRPIQMSFTTVQKQSY MKIEAIDVILVDVPASRP IOMSFTIVOKOS Y ee MKIEAIDVTLVDVPASRP IQMSFTIVOKOS Y MKIEAIDVILVDVPASRP IOMSFTTVOKOS MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY MRIESITATIVDVPTRRPLOMSFTTVNKQSY E Q User Manual Marcin Joachimiak 1 6 04 0 Overview Jevtrace is a Java implementation of the Evolutionary Trace ET method and its variations Jevtrace expands on the ET method allowing detailed interactions with the underlying data as well
14. a PDB format file AA i E nm UN Figure 6 Selecting a valid PDB file will display the structure in WebMol Jevtrace aligns the sequence of the PDB structure with the selected sequence in the alignment This alignment is the basis for all subsequent sequence to structure mappings 5 2 Displaying alignment selections on the structure Any selections in the multiple alignment will be automatically displayed on the structure in WebMol The Structure menu has a Map Selected Sequence option that will only map selections of that specific sequence n 30 40 50 23174 T O x E MIATPVKIESVETIIBVDVI TISPHRLSVATMNC TI MIATPVKIESVETIMVELQTINPHRLSVATMNCITL MIATPVKIESVETIBVDV TISPHRLSVATMNC MIPSAVQIQAVETIMVDVETIRP peavey RI ITALANPQILGIETIMLDLYT INP HVLAMATMHAL T I MNAQITSVETVVDLYT IQA HOLAMATMOQHTL MNAQITSVEA IMVDL DT IMAHOL AMA TMOQNTT TAGMTATISSIEA IM DLTIDAHOLAMATMOQNTI E TOOSITAIESIEAI BVDLITIISPHOLAMATMOR TI MSOQAV LOSLES IfVDLYT INP HKLAMHTMNRG TL MSQAVIQSLES IfVDLETIN ERI li MSQVLIHSLSAIHVDLISTIZPHKLAMHTMOK DTEMNRILIENLSAIHVDLITIZPHKLAMHTMON MTSALIERIEAIHVDLI TISPHKLAMHTMOQ MKIEAIDVT VDVIASIUP IOMSFTTVOK IS Y MKIEAIDVT VDVIJASIUP IOMSFTTVOK US Y MKIEAIDVT VDVIJASIUPIOMSFTTVOK ISY MKIEAIDVT BVDVIJASISPIOMSFTTVOK ISY Figure 7 Selections in the sequence alignment are automatically displayed on the structure in WebMol The background in WebMol was ch
15. anged to white for higher contrast in the color menu top right of the WebMol window 5 3 Using multiple structures During a single session Jevtrace allows interaction with an unlimited number of protein structures however only one structure can be associated with the alignment at one time In order to associate a new structure with the alignment click on the previously selected sequence name to deselect it and select a new sequence name Then click Open WebMol and choose the new PDB file 6 Making Trees and Multiple Alignments Talk The tree functionality in Jevtrace allows use of branching and grouping information inherent in trees and phylogenetic trees 6 1 Selecting subfamilies in the tree 2 jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln MYKSVETILVD IPTIRPHKLSVTIMOTOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL MIATPVKIESVETILVDVPTIRPHRLSVATMNCOTL MIATPVKIESVETILVELPTIRPHRLSVATMNCOTL MIATPYKIESVETILVDVPTIRPHRLSVATMNC OTL MIPSAVOIQAVETILVDVPTIRPHRLSVATMNC OAL MTALANPQILGIETILLDLPTIRPHYLAMATMHAQTI MNAQITSVETVLVDLPTIRAHQLAMATMOQOOTL MNAQITSVEAILVDLPTIRAHQLAMATMQQOTL MHE TNLHGKGMTAGMTATISS IEAILVDLPTIRAHQLAMATMQOOTL MEKVATOOS ITAIES IEAILVDLPTIRPHOLAMATMOROTL MSQAVIQSLES ILIVDLPTIRPHKLAMHTMNROTL MSQAV IQSLES LIVDLPTIRPHKLAMHTMNRQTL T9MSOVLIHSLSAIIVDLPTIRPHKLAMHTMQKQTI MDTEMNRILIENLSAIIVDLPTIRPHKLAMHTMQNQ MTSALI
16. as results of the analysis The graphical interface allows protein family exploration in context of multiple sequence alignments phylogeny and protein structures Protein structure viewing and analysis is performed with WebMol which is integrated and distributed with Jevtrace Jevtrace reference JEvTrace refinement and variations of the evolutionary trace in JAVA Joachimiak MP Cohen FE Genome Biol 2002 3 12 RESEARCH0077 Epub 2002 Nov 26 Selected Evolutionary Trace references Structural clusters of evolutionary trace residues are statistically significant and common in proteins Madabushi S Yao H Marsh M Kristensen DM Philippi A Sowa ME Lichtarge O J Mol Biol 2002 Feb 8 316 1 139 54 An evolutionary trace method defines binding surfaces common to protein families Lichtarge O Bourne HR Cohen FE J Mol Biol 1996 Mar 29 257 2 342 58 1 Installation A Jevtrace requires a working Java Runtime Environment JRE The Sun Microsystems J2E version 1 4 2 or the most current version is recommended please do not use Java version 1 4 1 which has graphical problems Note If you are using Windows or Macintosh it is likely that the operating system has a default Java setup To check what version you are running type java version on the command line Mac OS X stores previous versions of Java in the System directory B Please fill out the Academic Software Licensing form and fax it to Erik Ellestad at 415 476
17. at position Show correlation score after ET or correlation analysis shows the pairwise subfamily score Show lowest rank score after ET analysis shows the lowest phylogenetic rank for that column Convert score to column scoring after ET or correlation analysis converts the column scoring to coloring of the entire column for example this is necessary to output coloring compatible to Chimera Remove score after ET or correlation analysis removes the column scoring altogether d Structure Open WebMol prompts for a PDB file through a file dialog Loads the selected PDB file and aligns the PDB sequence to the selected sequence in the alignment If the alignment is successful associates the structure with the alignment and displays it in WebMol WebMol buried exposed routine calculates the residue solvent accessibility in WebMol Buried residues are represented by thin lines and exposed residues as thick lines Note the following two options can be combined Map Selected Sequence maps only positions for which this sequence is selected excluding columns Map Selected Columns maps only selected columns e MSA Color Conserved Positions colors absolutely conserved positions red Color variable positions colors not absolutely conserved positions blue Color gapped positions colors gapped positions green Color positions by percent sequence identity colors all the positions in the alignment using t
18. ce identity over all non gapped residues for each subclade Annotate with branch length annotates the tree with the branch lengths Show consensus for selected nodes displays the computed consensus sequences for any node s selected in the tree Color Positions Conserved Below Node finds all positions in the selected subclades that are conserved within those subclades and different between them Trace parents of a node for a selected node traces the sequence conservation in up to eight ancestors parents Read tree selections from file reads a text file with encoding all of the tree graphical selections Write tree selections to file writes a text file with encoding all of the tree graphical selections Average percent sequence identity in partition s for the selected partitions computes and displays the average percent sequence identity of all the nodes in that partition Min Max sequence identity in partition s for the selected partitions computes and displays the minimum and maximum percent sequence identity of all the nodes in that partition Export MSA graphics JPEG exports the alignment with colored selections to a JPEG file c ET Use MSA selection during ET or correlation analysis uses only the selected alignment columns for computations Convert to absolute sequence variability after ET or correlation analysis normalizes the column score by the absolute sequence variability at th
19. enalties and weight matrix choice Nucleic Acids Res 1994 Nov 11 22 22 4673 80 Notredame C Higgins DG Heringa J Related Articles T Coffee A novel method for fast and accurate multiple sequence alignment J Mol Biol 2000 Sep 8 302 1 205 17 Katoh K Misawa K Kuma K Miyata T Related Articles MAFFT a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res 2002 Jul 15 30 14 3059 66 FASTME Desper R Gascuel O Related Articles Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least Squares Tree Fitting Mol Biol Evol 2003 Dec 23 Howe K Bateman A Durbin R Related Articles QuickTree building huge Neighbour Joining trees of protein sequences Bioinformatics 2002 Nov 18 11 1546 7 3 Starting Jevtrace Jevtrace allows interaction with the following types of data Sequence Phylogeny Protein alignment Structure Sequence alignment Yes Yes Yes Phylogeny Yes Yes Indirectly Protein Structure Yes Indirectly Yes Crosstalk between different sequence alignments is achieved using a function to translate results including graphical selections from one alignment to another At least one common identical sequence has to be present in both alignments Crosstalk between different phylogenies or trees is currently not implemented in Jevtrace Please re
20. ent sequence identity of all sequences below each node This is done using the Annotate with ungapped sequence identity function in the Tree menu Alternately the branch distances from the original tree or tree file can be displayed using the Annotate branch length in the Tree menu amp jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln MYKSVETILVD IPTIRPHKLSVTIMOTOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCOQTI MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL MIATPVKIESVETILVDVPTIRPHRLSVATMNCQTI MIATPVKIESVETILVELPTIRPHRLSVATMNCQ MIATPVKIESVETILVDVPTIRPHRLSVATMNCQ MIPSAVOIQAVETILVDVPTIRPHRLSVATMNCOQA MTALANPOILGIETILLDLPTIRPHVLAMATMHAQTI MNAQITSVETVLYDLPTIRAHQLAMATMQOOTL MNAQITSVEAILVDLPTIRAHQLAMATMOQQ MHE TNLHGKGMTAGMTATISS IEAILVDLPTIRAHQLAMATMQQQ MKVATOOS ITAIES IEAILVDLPTIRPHOLAMATMOROTL irri ied MSQAVIQSLESIIVDLPTIRPHKLAMHTMNROTI MSQAVIOSLESIIVDLPTIRPHKLAMHTMNRQ MSOVL IHSLSALIVDLPTIRPHKLAMHTMOKO MDTEMNRILIENLSAIIVDLPTIRPHKLAMHTMQNQ T MTSALIERIEAIIVDLPTIRPHKLAMHTMQQO MTSALIERIDAIIVDLPTIRPHKLAMHTMQQQ MSQVLIESVETIIVDLPTIRPHKLAMHTMQHQ MKIDAIEAVIVDVPTKRPIQMSITTVHOOSY MKIDAIDALIVDVPTRRP IOMSMTTVHOOS Y MKIEAIDVTLVDVPASRPIQMSFTTVOKQSY MKIEAIDVTLVDVPASRPIOMSFTTVOKQSY MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKOSY MKIEAISTTIVDVPTRRPLOMSFTTVHKQS w MRIES DEAT IVDVP Teer TTVNKOSYX
21. fer to phylogenetic reconstruction packages like PAUP or PHYLIP for methods to compare and analyze multiple trees 3 Crosstalk between phylogenies and structures and vice versa is achieved indirectly through the sequence alignment data and WebMol Protein structure viewing and most analysis are delegated to WebMol The following are the command line startup options for Jevtrace java jevtrace jevtrace java jevtrace jevtrace session file gt java jevtrace jevtrace alignment file gt java jevtrace jevtrace tree file gt java jevtrace jevtrace tree file gt alignment file gt java jevtrace jevtrace tree file gt alignment file lt pdb file gt 4 Talking to the Multiple Alignments Jevtrace can be run with sequence data alone The sequences can be in Fasta format aligned or unaligned or in the ALN alignment format used by programs such as ClustalW ClustalX and t_coffee The sequence only mode of Jevtrace is especially useful when the set of sequences is large when one is trying to prune the sequence set for example removing redundant or spurious hits from a database search or when phylogenetic and structure data are not available Jevtrace allows an array of interactions with the sequence data including a number of editing features Details of editing functionalities can be found in section 7 One example of Jevtrace sequence analysis functionality is the ability to generate colored images of entire alignments as
22. g on a graphical object selects and clicking again deselects TREE single node selection mouse click on node in tree subfamily selection for analysis hold ctrl key and mouse click on the parent node of a subclade graphical highlighting of a subfamily hold shift key and mouse click on a node NAME CANVAS sequence name mouse click on a name A selected name is required for opening a protein structure Multiple names can be selected for multiple alignment editing and analysis ALIGNMENT CANVAS single amino acid mouse click over amino acid in multiple alignment alignment column selection mouse click above the column in the region of sequence numbering B Buttons Clear Tree Create Partitions enables creation of partitions of the phylogenetic tree Partitions are created by clicking on the tree canvas Up to eight partitions can be created in any order they will sorted by Jevtrace from left to right ET based on user selected partitions defined above in Create Partitions or a set of selected nodes performs the Evolutionary Trace computation The results will be shown on the sequence alignment and structure if it is associated The score for each column is shown above the sequence alignment Correlations based on a set of selected nodes performs a evolutionary correlation computation The results will be shown on the sequence alignment and structure if it is associated The score for each column is
23. he Jevtrace color scheme green to red where red is absolutely conserved gt 99 red gt 89 magenta gt 79 gt 69 orange gt 59 yellow gt 49 cyan gt 39 blue gt 29 gray lt 29 green Make sequences by pairwise identity a dialog prompts for the percent sequence identity cutoff For any pair of sequences with identity above the cutoff the second sequence will be removed Filter sequences by minimum ungapped length a dialog prompts for the minimum ungapped length cutoff All sequences below the minimum are discarded Define similarity relative to tree selection for the selected sequence computes the unique residues relative to other sequences Define specificity relative to tree selection discrete for the selected sequence computes the unique residues relative to other sequences Define specificity relative to all for the selected sequence computes the unique residues relative to other sequences Write in Fasta format outputs the current alignment to a Fasta format file Write alignment in ClustalW format aln outputs the current alignment to a Clustalw aln format file Write alignment in Nexus format nexus outputs the current alignment to a MSF format file Write alignment in Phylip format phylip outputs the current alignment to a MSF format file Export MSA graphics JPEG exports the alignment with colored selections to a JPEG file
24. iting functions are in the MSA editing menu Any result of an editing function can be reverted to the previous state one step back in the history by choosing the Revert to previous sequences option To remove a character or characters simply select them in the alignment and choose the Remove character s option Jevtrace will automatically pad the appropriate sequences with gaps at the end to preserve the alignment format Remove selected columns and Remove not selected columns will perform the obvious operations based on the selected columns Remove selected sequences and Remove not selected sequences will perform the obvious operations based on the selected sequence names To add a gap character select a character characters or columns and choose Add gap before This will place gaps before any selections and will automatically pad the appropriate sequences with gaps at the end to preserve the alignment format Left inclusive column cut and Right inclusive column cut will remove all columns to the left or to the right of the selected column a single column selection is required 4 3 Sequence properties The Sequence Properties menu provides analysis and graphical views of chemical and physical property analysis of the sequence data The available properties include molecular mass from Proteins Creighton 2 Edition molecular volume from Proteins Creighton 2 Edition electronegativity
25. le Sequence Alignments MSA Jevtrace is compatible with the CLUSTALW aln FASTA and PILEUP msf sequence alignment formats Currently the t_coffee multiple alignment program is suggested for accurate but slow alignments especially cases of remote similarity CLUSTALW X is recommended for somewhat less accurate but much faster alignments MAFFT is a newer multiple alignment algorithm that is even faster than CLUSTALW X however no tree results are provided B Phylogeny and trees Jevtrace is compatible with the Newick ph dnd and GCG figure tree formats The PHYLIP and PAUP software packages are suggested for phylogenetic tree reconstruction from protein sequence data Some reliable and fast Neighbor Joining methods for large data sets are FASTME and QuickTree The methods mentioned in A will provide the input multiple alignment data for the phylogenetic analysis In many cases trees calculated from sequence similarity such as the the dnd output of the CLUSTALW progressive multiple alignment can provide reasonable approximations of evolutionary relationships However whenever possible evolutionary data based on phylogenetic models is desired C Protein Structure PDB format files are compatible with Jevtrace and WebMol References Thompson JD Higgins DG Gibson TJ Related Articles CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting position specific gap p
26. log will report any discrepancies in most cases the association will still be performed If the file format is valid WebMol will display the structure 5 1dbx_50 aln a 1dbx_50 dnd la 1dbx_50 fasta E 1dbx_60 aln a 1ALU nr human figure Sa 60 dnd ls LALU nr human msf a idbx 60 fasta E MYKSVETILVDIPTIRPHKLSVTIMOTOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL IATGITIDRIDTLLVDVPTVRPHKLSVATMNCQTI IATPVKIESVETILVDVPTIRPHRLSVATMNCQTI MIATPVKIESVETILVELPTIRPHRLSVATMNCOTL MIATPVKIESVETILVDVPTIRPHRLSVATMNCQ MIPSAVOIQAVETILVDVPTIRPHRLSVATMNC MTALANPOILGIETILLDLPTI Vespa been MNAQITSVETVLVDLPTIRAHOLAMATMOOOTL MNAQITSVEA ILVDLPTIRAHOLAMATMOQOTI AGMTATISSIEAILVDLPTIRAHOLAMATMOOO MEVATOOSITAIESIEAILVDLPTIRPHOLAMATMORO MSQAVIQSLES LIVDLPTIRPHKLAMHTMNRQ MSQAVIOSLES LIVDLPTIRPHKLAMHTMNRO MSOVLIHSLSAIIVDLPTIRPHKLAMHTMOKOTL EMNRILIENLSAIIVDLPTIRPHKLAMHTMQNO MTSALIERIEAIIVDLPTIRPHKLAMHTMQQO MTSAL IERIDAIIVDLPTIRPHKLAMHTMQQQ MSQVLIESVETIIVDLPTIRPHKLAMHTMQRHQ eee MRIDAIEAVIVDVPTERP IOMS ITTVHOOS Y MEIDAIDALIVDVPTRRP IOMSMTTVHOOS Y MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY MKIEAIDVTLVDVPASRPIOMSFTTVOKQOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKOSY MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY 7 MKIEAISTTIVDVPTRRPLOMSFTTVHKOQSY Aa o i aos as pra pas a ae E Figure 5 After selecting the sequence to be associated with a protein structure mouse clicking on the Open WebMol button will open a file dialog prompting for
27. lumn in the alignment will select that column or deselect if already selected amp jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln MYKSVETILVD IPTIRPHKLSVTIMOTOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCOTL MIATGITIDRIDTLLVDVPTVRPHKLSVATMNC OTL MIATPYKIESVETILVDVPTIRPHRLSVATMNCOTL MIATPYKIESVETILVELPTIRPHRLSVATMNCOTL MIATPVKIESVETILVDVPTIRPHRLSVATMNC OTL wwwMIPSAVOIQAVETILVDVPTIRPHRLSVATMNCQAL MTALANPQILGIETILLDLPTIRPHVLAMATMHAQTI MNAQITSVETVLYDLPTIRAHOLAMATMOQOTI MNAQITSVEA ILYDLPTIRAHOLAMATMOQOTI MHETNLHGKGMTAGMTATISSIEAILVDLPTIRAHQLAMATMOQOTI MKVATOOSITAIESIEAILVDLPTIRPHOLAMATMQRO T MSQAVIOSLESIIVDLPTIRPHKLAMHTMNRQ MSQAVIOSLESIIVDLPTIRPHKLAMHTMNROTI MSOVLIHSLSAIIVDLPTIRPHKLAMHTMOKOTI EMNRILIENLSAIIVDLPTIRPHKLAMHTMONO MTSALIERIEAIIVDLPTIRPHKLAMHTMQQQ MTSALIERIDAIIVDLPTIRPHKLAMHTMQQQ MSQVLIESVETIIVDLPTIRPHKLAMHTMOHQ MKIDAIEAVIVDVPTKRPIOMSITTVHOOSY MKIDAIDALIVDVPTRRP IOMSMTTVHOOS Y MKIEAIDVTLVDVPASRPIOMSFTTVOKOSY MKIEAIDVTLVDVPASRPIQMSFTTVOKQSY MKIEAIDVTILVDVPASRP IOMSFTTVOKOS MKIEAIDVTLVDVPASRPIOMSFTTVOKQOSY MKIEAIDVILVDVPASRP IOMSFTTVOKOS MKIEAISTTIVDVPTRRPLOMSFTTVHKQOS Y MKIEAISTTIVDVPTRRPLOMSFTTVHKQSY T MRIESITATIVDVPTRRPLOMSFTTVNKQSY OKVESRILDVPLIRPHGFA E Figure 4 Clicking on any sequence name in the middle orange panel will select that sequence column or deselect if already selected 4 2 Editing alignments All of the alignment ed
28. milies selected in Figure 1 simply click on the Correlations button amp jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace testVMLE tcoffee aln MYKSVETILVDIPTIRPHK SVTTIQTO MIATGITIDRIDTLLVDVPTVRPHK SVATINCQ MIATGITIDRIDTLLVDVPTVRPHK SVATINCQ MIATPVKIESVETILVDVPTIRPHRESVATINCO MIATPVKIESVETILVELPTIRPHR SVATINCQ MIATPVKIESVETILVDVPTIRPHRESVATONCQ MIPSAVOIQAVETILVDVPTIRPHRESVATINCOS MTALANPOILGIETILLDLPTIRPHV AMATTIHAQTI MNAQITSVETVLVD PTIRAHQMATIOOQ MNAQITSVEAILVD BPTIRAHQEEMATIOOQJU MHETNLHGKGMTAGMTATISSIEAILVDIBPTIRAHQEMATIOOQG MKVATQOSITAIESIEAILVD PTIRPHQMATIORQNI MSQAVIOSLESIIVD PTIRPHKEMHTINROQH MSQAVIOSLESIIVD PTIRPHKUEMHTINROGNI MSOVLIHSLSAIIVDPTIRPHKEMHTIOKQU MTSALIERIEAIIVD PTIRPHKEMHTIOOQUN MTSALIERIDAIIVDIBPTIRPHE wHTIOOQU MSQVLIESVETIIVDIBPTIRPHEWNEMHTIOHQU MKIDAIEAVIVDWPTKRP IOMS ITTWHOO MKIDAIDALIVD PTRRP IOMSMTTWHOG MKIEAIDVTLVDMPASRPIOMSFTTWOKO MKIEAIDVTLVDMPASRPIQMSFTTWOKO MKIEAIDVTLVDMPASRPIOMSFTTWOKO MKIEAIDVTLVDWPASRPIOMSFTTVOKO MKIEAIDVTLVDMPASRPIQOMSFTTWOKO MKIEAISTTIVDWPTRRPLOMSFTTWHKO MKIEAISTTIVDWPTRRPLOMSF TTWHKO MRIESITATIVD PTRRPLOMSF TTWNKO OKVESRILDYPLIBPHCFA Figure 10 Results of evolutionary correlation analysis based on the subfamilies selected in Figure 8 6 3 Jevtrace analysis using selected partitions the Evolutionary Trace The original Evolutionary Trace method relies on creating pa
29. ompute the Evolutionary Trace residues for the selected phylogenetic partitions Performance and approximate runtime will be monitored with a progress bar MYKSVETILVDIPTIRPHKLSVTTMQTOTI MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCOQTI MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQTI MIATPVKIESVETILVDVPTIRPHRLSVATMNCQTI MIATPVKIESVETILVELPTIRPHRLSVATMNC QTL MIATPVKIESVETILVDVPTIRPHRLSVATMNCQTL MIPSAVOIQAVETILVDVPTIRPHRLSVATMNCOAI ITALANPQILGIETILLDLPTIRPHVLAMATMHAQTI MNAQITSVETVLVDLPTIRAHQLAMATMQQQ MNAQITSVEAILVDLPTIRAHQLAMATMQQQ ITAGMTATISSIEAILVDLPTIRAHQLAMATMOOOTI ATOOSITAIESIEAILVDLPTIRPHOLAMATMOROTI MSQAVIQSLESIIVDLPTIRP HKLAMHTMNROTL MSQAV IOSLES I IVDLPTIRPHKLAMHTMNROTL MSQVLIHSLSAIIVDLPTIRP HKLAMHTMQKOTL DTEMNRILIENLSAIIVDLPTIRPHELAMHTMONO MISALIERIEAIIVDLPTIRPHELAMHTMOOO MISALIERIDAIIVDLPTIRPHKLAMHTMOOO MSQVL IESVETI IVDLPTIRPHKLAMHTMOHO MKIDAIEAVIVDVPTKRPIOMSITIVHOOSY MKIDAIDALIVDVPTRRP IOMSMTTVHOOS MKIEAIDWVTLVDVPASRPIOMSETTVOKOSY MKIEAIDVTLVDVPASRPIQMSETTVQKOSY MKIEAIDWTLVDVPASRPIQOMSETTVOKOSY MKIEAIDVTLVDVPASRPIOMSETTVOKOSY MKIEAIDWILVDVPASRP IOMSETTVOKOS MKIEAISTTIVDVPTRRPLOMSETTVHKOSY MKIEAISTTIVDVPTRRPLOMSETTVHKOSY 14 The Evolutionary Trace results will be shown as colored selections on the alignment and as colored residues on the structure if the structure has been previously opened in WebMol see Section 5 1 7 Dictionary of Menus and Features A Graphical Selections In all cases clickin
30. rtitions of the phylogenetic tree This procedure has been difficult to automate Also the use of percent sequence identity may be misleading since evolutionary models rely on more subtle measures of sequence similarity and distance Jevtrace allows creation of up to eight partitions anywhere on the phylogenetic tree The partitions can be created in any order Jevtrace will sort them left to right when computing the Evolutionary Trace analysis ET button amp jevtrace dendogram c jevtrace_test MLE_tcoffee ph MSA c jevtrace_test MLE_tcoffee aln AVWAGARLADAGYSLVEQP IAAANRAGLKRLTALAH IP IMADEALHGPYDAFALAF AIWAGKRFADASVAL IEOP IAAENRAGLKRLTDLAQ VP IMADEALHGPADAFALAS RIWAGKRFAEAGVAL EOP IAAENRAGLKRLTDLAQ VP IMADEALHGPADAFALAS 230 240 250 260 270 280 VKGIQOQOLODGGIDLIEQPCAIENTDALARLTARFD VAIMADEVLTGPDSAYRIAE LN PVWAGARLADAGVSLVEOP IAAANRAGLKRLTALAH IP IMADEALHGPYDAFALAF ALWACERLADAGCNL EOP IAADDRRGLKRLTHHSK VP IMADEALHGPYDAFDVAS ARRGLAMLADAGCDLVEQP I IRHNRDGMARLVALGL VPVMADESLTGPASAMDFAF ATLGIQALEAAGIDL IEQPTPREORGVLARLSARF I VP IMADEAVTGPEDALELVE RALGIEALQAAGIDLIEQPTPREQRGALARLAARFI VPIMADEAVTGPEDALELVE RATGIAMLEAAGIDLIEQPTPREQORTALARLAARFV VPIMADEAVTGPEDAMELAF RATGIAMLETAGIDLIEQOPTPREQORAALARLAARFV VPIMADEAVCGPEDAMELAF ORACATLGDNGIALIEQPIARHNRVGLARLSSRGG APIMADEAIESVEDAFHLAF RORACATLGDNGIAL IEQP IARHNRIGLARLSSRGG AP IMADEAIESVEDAFHLAF A IRGCOVLGENGIDLIEQPISRVNRSGOVRLNORGP AP IMADESIESVEDAFSLA RIRGCRVLGDNGIDLIEQPISRVNRS
31. structures The Jevtrace coloring scheme consists of eight colors which can be uniquely displayed and shaded on graphical representations of protein structure This coloring scheme is also used as a color scale for scores generated by computations Pairs of Subfamilies Pairwise Subfamily Score case lt 8 Mapped to Integer Interval Maximum Invariance 1 pair 1 pair Minimum Invariance of subfamilies of subfamilies d Maximum pairs of subfamilies The color scale used in Jevtrace The scale is used both to show cardinality e g the left to right order of phylogenetic partitions but also scores generated by computation Figure 1 Mouse clicking on any character will select that character Clicking again will deselect it evtrace_test MLE_tcoffee ph MSA c jevtrace_test 30 40 MYKSVETILVDIPTIRPHELSVTIMOTO MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ MIATGITIDRIDTLLVDVPTVRPHKLSVATMNCQ MIATPVKIESVETILVDVPTIRPHRLSVATMNCQ MIATPVKIESVETILVELPTIRPHRLSVATMNCQ MIATPVKIESVETILVDVPTIRPHRLSVATMNCQ MIPSAVQIOQAVETILVDVPTIRPHRLSVATMNCQA MTALANPQILGIETILLDLPTIRPHVLAMATMHAOTI e MNAQITSVETVLVDLPTIRAHOLAMATMOQO MNAQITSVEA ILYDLPTIRAHOLAMATMOQO MHETNLHGKGMTAGMTATISSIEAILVDLPTIRAHQLAMATMQQQ Mem rece MKVATOOS ITAIES IEAILVDLPTIRPHOLAMATMORQ MSQAVIQSLESIIVDLPTIRPHKLAMHTMNRQ MSOAVICOBLESIIVDLPTIRPHKLAMHTMNRQ SLSAIIVDLPTIRPHKLAMHTMOKQ ENLSAIIVDLPTIRPHKLAMHTMQNQ ERIEAIIVDLPTIRPHKLAMHTMQQQO SALIERIDAIIVDLPTIRPHKLAMHTMQQQO
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