MEGA-MD User Manual
Contents
1. UCSC Genome Browser Database Fujita P A et al The UCSC Genome Browser database update 2011 Nucleic Acids Research 2011 39 D876 D8822. identifiers as well as mutant and reference alleles are given here Note mutant amino acids that are appended with an asterisk have multiple rows returned by the MEGA MD server each row indicating a mutation at the nucleotide level look to the Coordinate Info band to see nucleotide change e Predictions consensus EvoD PolyPhen 2 and SIFT predictions are given here Where both the original and balanced predictions are given for PolyPhen 2 and SIFT balanced predictions are described in Liu and Kumar 2013 e Impact the impact scores for EvoD PolyPhen 2 and SIFT predictions are provided along with the Grantham distance and Blosum62 value e Evolutionary Features hidden by default substitution rate position time span and mutation time span are displayed see below for a description of how to display this band e Coordinate Info hidden by default additional coordinate information is shown here including chromosome strand nucleotide position amino acid position wild nucleotide and mutant nucleotide see below for a description of how to display this band To toggle on off the display of a given band click on the indicator button which is located to the far left in the band headers row A popup menu will appear from which bands can be selected deselected Often times when changing the display of bands column widths will change in undesirable ways To remedy this you can execute the Best fit Columns action by c
3. the amino acid position is specified by selecting the site of interest which will be highlighted With the site of interest selected the mutant allele or all alleles can be specified from the Diagnose Variant drop down list When an allele is selected from the list MEGA MD will query the MEGA MDW server and append the returned predictions and related data to the Mutation Explorer Predictions tab The Sequence Data Explorer window also provides much other functionality such as alignment export and composition based exploration Analysis Preferences Dialog T Seque ce Data Explorer D 00252 NM 6 0261 Data Display Search Groups Highlight Statistics Help a 2 ala a seles o gt Specias A A E Diagnose variant seere EName NS AFA a aL i A All 1 Human SV I HNLQRMIDSSTQRLDLEAT Gian 2 Chimp SVIHNLQRDSSTQRLDLEAT R Arginine 413 Gorilla SVIHNLQRDSSTQRLDLEAT N Asparagine 44 Orangutan SVIRNLQRDSSTQRLDLEAT D Aspartic Acid 5 Rhesus SVIHNLQKIDSSTQRLDLEAT ES 6 Baboon SVIHNLQKDSSTQRLDLEAT O Chaara 7 Marmoset SVIHNLQRDSSTQRLDLEAT EPE Ee 8 Tarsier AAIHDLQRDSSTQRTDLEAA pes A9 Mouse Lemur SA I HDLQRDSSSQRADLESA SEAS 110 Bushbaby S VI HDLQRDSSAQRADLEST 4111 Tree Shrew oer he boa So ee L oleucme 112 Mouse SATODL SSIQHADLEST A 4 Ly K Lysine rs F Phenylalanine aa SEMEL ES
4. 9 MouseLemu SA l1HDLQRDSSSQRADLESA EOS ESRLHLLT 4110 Bushbaby SV IHDLQRDSSAQRADLEST ESA LARA v11 Tree Shrew Se ee A A 1 Isoleucine ete Sr ve oes 4112 Mouse SA 18D L DSSIQHADLES TMB E SL LHM T I K ld K Lysine E F Phenylalanine 707305 Highlighted None Data P Proline References dbNSFP Liu X Jian X Boerwinkle E dbNSFP a lightweight database of human nonsynonymous SNPs and their functional predictions Hum Mutat 2011 32 8 894 9 doi 10 1002 humu 21517 MEGA MD Kumar S Sanderford M Gray VE Ye J Liu Li Evolutionary diagnosis method for variants in personal exomes Nature Methods 2012 Sep 9 9 855 6 doi 10 1038 nmeth 2147 Liu L and Kumar S Evolutionary balancing is critical for correctly predicting amino acid variants with functional impact Molecular Biology and Evolution 2013 30 1252 1257 MEGA Molecular Evolutionary Genetics Analysis Tamura K Stecher G Peterson D Filipski A and Kumar S MEGA6 Molecular Evolutionary Genetics Analysis version 6 0 Molecular Biology and Evolution 2013 30 2725 2729 PolyPhen2 Adzhubei IA Schmidt S Peshkin L Ramensky V Gerasimova A Bork P Kondrashov A Sunyaev S A method and server for predicting damaging missense mutations Nature Methods 2010 7 248 249 SIFT Pauline C Ng and Steven Henikoff SIFT predicting amino acid changes that affect protein function Nucl Acids Res 2003 31 13 3812 3814 doi 10 1093 nar gkg509
5. If the ML approach is selected the Analysis Preferences Dialog is displayed from which the analysis can be launched with custom settings e g substitution model distribution of rates etc If the MP approach is selected the analysis is launched immediately as not custom settings are available for this method When the analysis is completed the reference topology will be displayed in the Tree Explorer along with inferred ancestral alleles for the amino acid site designated earlier amp Detail View ie fot 633 Explore Alignment EN Explore Ancestors X Property Value Mutations rsID 2234926 Peptide ID NP_000252 mRNA Accession NM_000261 Reference AA R Mutant 4 4 K Predictions Consensus Likely Deleterious gt EvoD P value 2 7E 003 PolyPhen 2 Deleterious PolyPhen 2 Balanced Deleterious SIFT Deleterious SIFT Balanced Deleterious Impact EvoD Ta PolyPhen 2 1 0 SIFT 0 0 Grantham Distance 26 Blosum 62 2 Evolutionary Features Substitution Rate 0 96 Position Time Span 3110 45 Mutation Time Span 252 20 Coordinate Info Chromosome chr1 Chromosome Position 171621525 Strand Nucleotide Position 227 AA Position 76 Wild Nucleotide G Mutant Nucleotide A Sequence Data Explorer The Sequence Data Explorer is used to display the 46 species alignment for a given gene and provides a graphical interface for specifying amino acid position and mutant allele for nsSNVs of interest With an alignment activated
6. R Pika Si R nr Squirrel 4 T TreeLength 2412 Input Data Overview In order to retrieve predictions for a given nsSNV MEGA MD requires three pieces of information 1 RefSeq protein id e g NP_000082 2 amino acid position e g 43 3 mutant allele e g R There are two ways to provide this coordinate information to MEGA MD Upload a text file Use the interactive Wizard via Gene Search and integrated Sequence Data Explorer Upload a text file with the coordinate information for all nsSNVs of interest Create a text file with coordinate information for all nsSNVs to be explored following the format below NP_000758 99 E NP_000761 264 M NP_000762 144 C NP_000762 335 W NP_000773 374 T NP_000838 71 L NP_000886 131 H NP_000887 271 T Each line contains coordinate information for one nsSNV and each value is separated by white space i e spaces or tabs In the Mutation Explorer window select File gt Import Query Data From File or click the upload data button and browse for the newly created text file MEGA MD will first validate the format of the coordinate information file and then request prediction information for all specified nsSNVs from the MEGA MDW web server As data is retrieved the Mutation Explorer window is updated The MEGA MD application has no limit on the number of entries that can be included in the coordinate information file However depending on your internet conne
7. the 46 species reference phylogeny along with the 46 species peptide alignment for the relevant gene obtained from the UCSC resource MEGA MD is developed using the MEGA Molecular Evolutionary Genetics Analysis software package Citing MEGA MD Stecher G Tamura K Sanderford M Peterson D Liu L Kumar S MEGA MD Molecular Evolutionary Genetics Analysis software for mutational diagnosis of amino acid variation Bioinformatics 2013 submitted Disclaimer Although the utmost care has been taken to ensure the correctness of the software it is provided as is without any warranty of any kind In no event shall the authors or their employers be considered liable for any damages including but not limited to special consequential or other damages The authors specifically disclaim all other warranties expressed or implied including but not limited to the determination of the suitability of this product for a specific purpose use or application Copyright Copyright 2013 This software is protected under copyright law No part of this manual or program design may be reproduced without written permission from the copyright holders Please e mail all inquires to s kumar asu edu Development Team Glen Stecher e MEGA MD desktop client e MEGA MDW web application Koichiro Tamura e MEGA MD desktop client Maxwell Sanderford e MEGA MDW database administration e EvoD calculation pipeline developer
8. A MD application has no limit on the number of entries that can be included in the coordinate information file However depending on your internet connection speed and the current load on the MEGA MDW server retrieval of many predictions may take some time anything less than 5 000 should not be problematic For situations where MEGA MD does not perform optimally due to high numbers of nsSNVs the MEGA MDW can be used directly www mypeg info MEGA MDW The same text file can be uploaded to the MEGA MD server which will process the file and send you an email for retrieving prediction data once the processing is complete Mutation Explorer The Mutation Explorer window displays predictions and data associated with the nsSNVs being explored and provides functionality for text searching sorting importing exporting formatting and gene search This window displays two main views each located on a separate tab Gene Search Tab Prediction Data Tab Y Mutation Explorer arim File Edit Format Search Options Windows Help Ha g t S2heo m also 2 0 Gene Search Predictions Mutations Predictions a Peptide ID mRNAID Reference Mutant Consensus EvoD EvoD PolyPhen 2 PolyPhen 2 SIFT AA AA P value Original Balanced Original NP_000068 NM_OOO077 R Likely Neutral Deleterious 2 8E 001 Neutral Neutral Neutral NP_000148 NM 000157 T l Likely Neutral Deleterious 7 3E 002 Neutral Neutral Neutra
9. Contents Description Aea eee Re he ef AL Le 2 Citing MEGAMD iii a Linton denned dvd sande 2 Disc Meri A S A E 2 CO A acaso 3 D v lopment TM tal 3 Modes for running MEGA MD ccccsssccececeseesesseaecececesseseaeaeceeeeesseseaaeseeeesseseeseeaeseeeessesseaaaeeeeseesensaes 3 Interactive WiZ Atala it bas 4 Load a text file with coordinate info ooconoccccnononcccnononcnonononcnonononcconono nono nono nnco non nn na noo nn ca naar nn ca nnan nn canos 4 Mutation Explore Ai aba 5 Gene Search tab ii A a ed wee 7 Predicas EOE E ENEE ORE EO NA 8 Mutation Detail VIEW siii AE EE E E EEEE NNE AAEN 9 Sequence Data Explorer tt E E A ESEE EE E E e A aE 10 Analysis Preferences Dialog cata ia 10 Tres Xplod A E ees E ORE E EE ae ieee ee a he ees 11 input Data Overview a eS 11 Upload a text file with the coordinate information for all nsSNVs of interest ooooccccccnonononaoncnnnnnnns 12 Specify the coordinate information using the integrated Sequence Data Explorer cccccnoncnnnncnco 13 Rede Ces da dale OENE E 14 DON Puccini ida adn EO T eideaveadevses E E E E ELE A E E 14 MEGA MD costa EE RI E O EA AEA ORO AO T E 14 MEGA Molecular Evolutionary Genetics Analysis c cccccsscccsssececsseeeecsesaeeecsesaececeesaeeeesesaeeeeeeaaes 14 POIVPREN2 o A es aio eed A O A E A R 14 O 14 Description Computational diagnosis of amino acid variants in the human exome is the first step in assessing the disruptive impacts of no
10. Dan Peterson e MEGA MDW web application Sudhir Kumar e Project Director Center for Evolutionary Medicine and Informatics Biodesign Institute Arizona State University ASU Tempe AZ 85287 2 School of Life Sciences ASU Tempe AZ 85287 Department of Biology Tokyo Metropolitan University Hachioji shi Tokyo 192 0397 Japan Modes for running MEGA MD When MEGA MD is started a prompt window is displayed that offers a choice of using an interactive Wizard for specifying variants of interest or just loading a text file with coordinate info for variants of interest formatted according to a simple format amp Select Run Mode sos ox MEGA MD Mutation Diagnosis Do you wish to specify coordinate information for variants of interest using the interactive wizard or via a text file What s This What s This Text File When using the interactive Wizard graphical tools are used for specifying coordinate data by 1 Searching a database for the genes which harbor variants of interest 2 Specifying amino acid positions of variants of interest using a graphical grid display of gene sequence data 3 Selecting amino acid mutations from a list When loading coordinate information via a text file the information in the file is validated and then predictions are automatically retrieved from the MEGA MDW server and displayed in the Mutation Explorer window Interactive Wizard MEGA MD provides an intera
11. Neutral Neutral NP_000819 NM_000828 R Q Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_001877 NM_001886 y M Likely Deleterious Neutral 6 1E 002 Deleterious Deleterious Deleterious NP_002283 NM_002292 N K Likely Neutral Deleterious 256 001 Neutral Neutral Neutral NP_002326 NM_002335 N D Likely Neutral Deleterious 1 2E 001 Neutral Neutral Neutral NP_002871 NM_002880 T Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_003680 NM_003689 A T Likely Deleterious Neutral 9 2E 002 Deleterious Deleterious Deleterious NP_003898 NM_003907 R Q Likely Neutral Deleterious 2 5E 001 Neutral Neutral Neutral NP 003997 NM_004006 T A Likely Neutral Deleterious 9 2E 002 Neutral Neutral Neutral 4 itt Displaying 22 results 43 mutations Mutation Detail View The Mutation Detail View window displays all available information for the currently active record selected in the Mutation Explorer window Additionally this window provides access to the 46 species reference alignment for the given gene as well as the ability to infer ancestral alleles using the Maximum Likelihood ML or Maximum Parsimony MP methods When the Explore Alignment button is clicked MEGA MD will retrieve the 46 species reference alignment from the MEGA MDW server and display it in the Sequence Data Explorer from where it can be exported or further exploration can be done When the Explore Ancestors button is clicked the choice of ML and MP methods are presented
12. P Proline mmmmmmmmmm 0000000000 m no rarrrrrrTr se pe A A Perr Tr TITTITTTITT p z DFIPOPDODOD rrrrerreereee AAWWAAAAASA j 1 4 The Analysis Preferences Dialog is used for specifying the substitution model to use as well as the distribution of rates for ML based ancestral sequence inference Options Summary Analysis Ancestral Sequence Inference Statistical Method Maximum Likelihood Substitution Model Substitutions Type Amino acid Model Method Rates and Patterns Rates among Sites Gamma Distributed G No of Discrete Gamma Categories Data Subset to Use Gaps Missing Data Treatment Use all sites Branch Swap Fiter Moderate X concel _ Help Tree Explorer The Tree Explorer displays the results of the ancestral sequence inference analyses When an ancestral sequence inference analysis is complete the 46 species reference phylogeny is displayed in the Tree Explorer with the inferred ancestral alleles for the nsSNV amino acid site shown The Tree Explorer provides many capabilities which are described in detail in the MEGA user manual which can be obtained from www megasoftware net manual pdf File Image Subtree View Compute Ancestors Caption Help mels 4 SGE i ce we 8 ae R Human E e F m R Gorilla pa R Orangutan iy k Rhesus te k Baboon SF R Marmoset R Tarsier g R Mouse Lemur E R Bushbaby E Tree Shrew Lo R Rabbit slo
13. ction speed and the current load on the MEGA MDW server retrieval of many predictions may take some time anything less than 5 000 should not be problematic For situations where MEGA MD does not perform optimally due to high numbers of nsSNVs the MEGA MDW can be used directly www mypeg info MEGA MDW The same text file can be uploaded to the MEGA MD server which will process the file and send you an email for retrieving prediction data once the processing is complete Specify the coordinate information using the integrated Sequence Data Explorer If a 46 species sequence alignment has been retrieved see Gene Search for a given gene the Sequence Data Explorer window can be used to first navigate to the amino acid site of interest and then specify a mutant allele Data Display Search Groups Highlight Statistics Help Ba aa Meal 4 es Clr 0 2 Specia 44 4h EF omonose vaca cts v Name Al a 1 Human SVIHNLQRDSSTQORLDLEAT A Alanine ESLLHQL THI 2 Chimp SVIHNLQRDSSTQRLDLEAT R Arginine ESLLHQLT 3 Gorilla SVIHNLQRDSSTQRLDLEAT a ESTABA LT 14 Orangutan SVIRNLQRDSSTQRLDLEAT eee ES LLHQALT 25 Rhesus SVIHNLQKDSSTQRLDLEAT E ESLLHAQLT 6 Baboon SVIHNLQKDSSTQRLDLEAT Gee ESLLHQLT 17 Marmoset SV IHNLQMDSSTQRLDLEAT SOE SL I HQL S 8 Tarsier AAITHDLQRDSSTQRTDLEAA Beas ESLUHRLS
14. ctive system for specifying the coordinate information for variants of interest when few variants are to be explored see here if exploring many variants When using the interactive system the Mutation Explorer window is displayed with the Gene Search tab selected In the search box on this tab you can enter a gene name gene product description RefSeq mRNA id or peptide id and then press enter or click the search button A request will then be sent to the MEGA MDW web server for a list of genes that match the given query All matches are then displayed in a table view below the search box This table view displays the gene name peptide id and gene product for all results returned by the MEGA MDW web server To specify the amino acid position and mutant amino acid s click the Diagnose Variant link in the same row that lists the gene which harbors the variant of interest After clicking this link the UCSC 46 species peptide alignment for the specified gene will be retrieved from the MEGA MDW web server and displayed in the Sequence Data Explorer window In this window you first specify the amino acid position for the variant of interest by clicking at that location in the alignment grid When doing so that column in the alignment grid will be highlighted and the position will be indicated on the Diagnose Variant button After the position is specified the mutant amino acid is specified by clicking the Diagnose Variant button which is located on t
15. he toolbar A drop down list is then displayed from which you can select a single mutant amino acid or all possibilities Once the amino acid position in the alignment and the mutant amino acid have been designated predictions and related data for that variant will be retrieved from the MEGA MDW web server and displayed in the Mutation Explorer window Load a text file with coordinate info When retrieving predictions for a significant number of variants the interactive Wizard system is cumbersome and so MEGA MD provides a second way to specify coordinate information for variants of interest Instead of using the interactive Wizard you can load a text file with coordinate information as follows Create a text file with coordinate information for all nsSNVs to be explored following the format below NP_000758 99 E NP_000761 264 M NP_000762 144 C NP_000762 335 W NP_000773 374 T NP_000838 71 L NP_000886 131 H NP_000887 271 T Each line contains coordinate information for one nsSNV and each value is separated by white space i e spaces or tabs In the Mutation Explorer window select File gt Import Query Data From File or click the upload data button and browse for the newly created text file MEGA MD will first validate the format of the coordinate information file and then request prediction information for all specified nsSNVs from the MEGA MDW web server As data is retrieved the Mutation Explorer window is updated The MEG
16. her MEGA MD windows on by default e Show Toolbar toggle on off the display of the toolbar on by default e Toggle Auto Column Width when off default a horizontal scroll bar is used to view columns that don t fit in the window When off the horizontal scroll bar is removed and all columns are squeezed into view Windows e Detail View Form show the Mutation Detail View window e Search for a Gene jump to the Gene Search tab in the Mutation Explorer window e Sequence Data Explorer show the Sequence Data Explorer window Help e Contents Display this help document e About show the About MEGA MD window Gene Search tab The Gene Search tab facilitates searching for genes by name keyword based on gene product or by RefSeq identifiers mRNA ID or Protein ID Search results limited to 1000 are displayed in a list view with cursory information and a link for retrieving the 46 species reference protein sequence alignment from the MEGA MDW server When a sequence alignment is retrieved it is displayed in the Sequence Data Explorer which can be used to specify the amino acid site and mutant allele for a nsSNV of interest Gene Search Search By Gene Name Gene Product or RefSeq ID mRNA ID or Peptide ID Gene Name Peptide ID Gene Product MYZAP NP_001018110 myocardium enriched Zo associated protein isoform 1 Diagnose Variant MEF24 NP_001124398 myocyte specific enhancer factor 24 isoform 2 Diagno
17. l F NP_000148 NM_000157 Y G Likely Neutral Deleterious 3 0E 001 Neutral Neutral Neutral b NM_000261 i K Likely Deleterious Neutral Deleterious Deleterious SII NP_000262 NM_000271 E N Likely Neutral Deleterious 2 5E 001 Neutral Neutral Neutral NP_000362 NM_000371 A A Likely Neutral Deleterious 1 5E 001 Neutral Neutral Neutral NP_000362 NM_000371 F L Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_000430 NM 000439 G R Likely Neutral Deleterious 1 0E 001 Neutral Neutral Neutral NP_000805 NM_000814 R H Likely Neutral Deleterious 2 1E 001 Neutral Neutral Neutral NP_000819 NM_000828 R Q Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_001877 NM_001886 Y M Likely Deleterious Neutral 6 1E 002 Deleterious Deleterious Deleterious NP_002283 NM_002292 N K Likely Neutral Deleterious 2 5E 001 Neutral Neutral Neutral NP_002326 NM_002335 N D Likely Neutral Deleterious 1 2E 001 Neutral Neutral Neutral NP_002871 NM_002880 S T Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_003680 NhM_003689 A it Likely Deleterious Neutral 9 2E 002 Deleterious Deleterious Deleterious NP_003898 NM_003907 R Q Likely Neutral Deleterious 2 5E 001 Neutral Neutral Neutral NP 003997 NM 004006 i A Likely Neutral Deleterious 9 2 002 Neutral Neutral Neutral 4 m Displaying 22 results 43 mutations The actions provided by the Mutation Explorer are divided into several categories and are accessed using the main men
18. licking Format gt Resize columns to best fit or clicking the toolbar button Alternatively columns widths can be adjusted by dragging their header edges The toolbar and main menu provide access to several actions for importing exporting data formatting the view sorting text search and setting view options r Ra Mutation Explorer o E mE Fil Mutations Eh Options Windows Help v Predictions V Impact gt a B gt fi ajo E j ga Evolutionary Features Ey HAL Coordinate Info Mutations Predictions a Peptide ID mRNAID Reference Mutant Consensus EvoD EvoD PolyPhen 2 PolyPhen 2 SIFT AA AA P value Original Balanced Original NP_000068 NM_000077 R LES Likely Neutral Deleterious 2 8E 001 Neutral Neutral Neutral NP_000148 NM_000157 T Likely Neutral Deleterious 7 3E 002 Neutral Neutral Neutral E NP_000148 NM_000157 Yy G Likely Neutral Deleterious 3 0E 001 Neutral Neutral Neutral gt NM_ 000261 RA K ly Deleterious Neutral 2 3 Deleterious Deleterious a NM_000271 5 N Likely Neutral Deleterious 2 5E 001 Neutral Neutral Neutral NP_000362 NM_000371 T A Likely Neutral Deleterious 1 5E 001 Neutral Neutral Neutral NP_000362 NM_O000371 F te Likely Neutral Deleterious 2 4E 001 Neutral Neutral Neutral NP_000430 NM_000439 G Rs Likely Neutral Deleterious 1 0E 001 Neutral Neutral Neutral NP_000805 NM_000814 R H Likely Neutral Deleterious 2 1E 001 Neutral
19. n synonymous single nucleotide variants nsSNVs on human health and disease MEGA MD Molecular Evolutionary Genetics Analysis Mutation Diagnosis is a client server application used to forecast the deleteriousness of nsSNVs using multiple methods and explore them in the context of the variability permitted in the long term evolution of the affected positions MEGA MD accesses a relational database MD DB resident on our servers that contains pre computed diagnoses and associated information for all possible mutations at all amino acid positions in the human exome We have included three primary methods PolyPhen 2 SIFT and EvoD of predicting the functional impact of amino acid variants The first two are the most popular methods and the third significantly improves the performance for nSNVs found at ultra conserved and at fast evolving positions Kumar et al 2012 The PolyPhen 2 and SIFT diagnoses were obtained from dbNSFP We have also included results from a multi method consensus diagnosis because they have been shown to be more reliable In this case we use the evolutionarily balanced see Liu and Kumar 2013 versions of PolyPhen 2 and SIFT diagnosis In addition to retrieving pre computed predictions for variants in the human exome MEGA MD provides a facility to infer ancestral states for the position where a given amino acid mutation is found Maximum parsimony and maximum likelihood approaches are supported by this utility which uses
20. se Variant MEF24 NP_001124399 myocyte specific enhancer factor 24 isoform 3 Diagnose Variant MEF24 NP_001124400 myocyte specific enhancer factor 24 isoform 4 Diagnose Variant MEF2C NP_001124477 myocyte specific enhancer factor 2C isoform 2 Diagnose Variant MEF2B NP_001139257 myocyte specific enhancer factor 2B isoform a Diagnose Variant MYOCD NP_001139784 myocardin isoform 1 Diagnose Variant MYOCD NP_001139785 myocardin isoform 3 Diagnose Variant MEF24 NP_001165365 myocyte specific enhancer factor 24 isoform 2 Diagnose Variant MEF2C NP_001180276 myocyte specific enhancer factor 2C isoform 3 Diagnose Variant MEF2C NP_001180277 myocyte specific enhancer factor 2C isoform 4 Diagnose Variant MEF2C NP_001180278 myocyte specific enhancer factor 2C isoform 5 Diagnose Variant MEF2C NP_001180279 myocyte specific enhancer factor 2C isoform 1 Diagnose Variant MEF2C NP_002388 myocyte specific enhancer factor 2C isoform 1 Diagnose Variant MEF24 NP_005578 myocyte specific enhancer factor 24 isoform 1 Diagnose Variant MEF2BNB MEF2B NP_005910 myocyte enhancer factor 2B isoform b Diagnose Variant MEF2D NP_005911 myocyte specific enhancer factor 2D Diagnose Variant Y m Predictions The Predictions tab displays all prediction data retrieved from the MEGA MDW server in a list view Complete information for the currently active record is displayed in the Mutation Detail View Columns of data are banded together into categories e Mutations
21. u bar or the main tool bar File e Import Query Data From File load coordinate information form a text file e Search for a Gene access the gene search page e Export Table to Excel File save all prediction data to an MS Excel file e Export Table to CSV File save all prediction data to a Comma Separated Values text file e Exit Close the application Edit e Copy copy selected values to the system clip board e Select All select all values in the table e Clear Table clear all data from the table Format e Increase Precision increase the precision of all numeric values in the table and also in the Mutation Detail View window e Decrease Precision decrease the precision of all numeric values in the table and also in the Mutation Detail View window e Resize Columns to Best fit resizes all columns in the table to achieve the best fit and optimize the view Useful when hiding showing columns and column widths change sub optimally note if there are many records in the table more than several thousand this operation may take a few moments or more during which time the window will be unresponsive Search e Find text search for values in the table e Find Next find the next value matching the search query search goes to the right and then down to the next row Options e Keep detail view on top toggle this action on off to keep the Mutation Detail View window from staying in front of ot
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