AROE User Manual
Contents
1. sue 17 2 4 An AROE session tme 20 Confidential Proprietary Information Page 2 of 20 sanofi pasteur List of Figures Fig re 1 Registration for new Users eso ede S UI Ta eee us 6 Figure 2 Approval of registration Je ce eae Dieu eee es deiude ae 7 881 8 Figure 4 Changing user Immfortmation eae eco ttes oo ie tette dece e et a Lee dade rte 9 Figure 5 Changing configuration file dito rie bie d c db rado sende eS 10 Figure 6 Monitoring ongoing JOBS 11 Figure 7 RNA Structure SCOFIBE 2 eai deter 13 Figure 8 RNA str ct re scoring bats hi eu hed Ralf daos 14 Irure 92 etie aeons ecd i reso es 16 Figure 10 Optimization analysis reply ed b qoc etum dee 16 Figure 11 List of request for optimization rd 17 Figure 12 Result of job finished 18 Fipure 13 Result of ongotng JOD qo deo pi rete dadas 19 Figure 14 Result of job finished abnormally eene enne 20 Confid2. Redbases are changed ones AROE sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group Score Optimization Search My Info Logout Detail information of job finished normally ter 1 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT TAACTTTAAGAAGGAGATATACATATGAGTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGG TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC CAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG EGDIHMSLVLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKV SGLOYRVFRIHLPDPNKFGFPDTSFYNPDTORLVWACVGVEVGRGOPLGVGISGHPLLNKLDDTEN 71 19 48 52 77 79 10 80 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT TAACTTTAAGAAGGAGABATACAMATG TCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGG TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC CAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG Figure 12 Res
3. GCGCGTACCAACATTTATTATCATGCGGGCACCAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAA CAAAATTCTGGTGCCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTCCGGATA CCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCGTGGCCAGCCGCTGGGCGTGGGC ATT AGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG Positions of motif 198 200 308 313 i e 20 23 109 113 _ GetPosition Indicate motif with and 1 RNAfold parameters Rescale energy parameters to temperature 3 tetraloops V no dangling end energies GU pairs at the end of helices Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 7 RNA structure scoring Confidential Proprietary Information Page 13 of 20 sanofi pasteur AROE Sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group demo Score Optimization Search My Info Logout Result What is score An equivalent RNAfold command line RNAfold d The optimal secondary structure in bracket notation is lt The score of your motif s is below motif 198 200 gt type 2 score 10 motif 308 313 gt type 2 score 10 total score 20 Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 8 RNA structure scoring result Confidential Proprietary Information Page 14 of 20 sanofi pasteur
4. 2 4 4 Logging out from the system An AROE session will be terminated by logging out gt Click Logout on menu Confidential Proprietary Information Page 8 of 20 sanofi pasteur 2 4 5 Changing user information This function enables a user to change his her information gt Click menu Change information as needed gt Type current password gt Tochange password type current password and new password A 0 E E sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group demo Score Optimization Search My Info Logout Help ID First aroe Last Name 0000 Password New Password Phone 1111 Email Joe Wanq sanofipasteur com Tel 416 667 2700 ext 3275 Figure 4 Changing user information Confidential Proprietary Information Page 9 of 20 sanofi pasteur 2 4 6 Changing configuration file Only administrators can access this menu gt Log into AROE with administrator account Click Configuration on menu gt Change original value of a key to desired new value Click Reload button in order to read original configuration file again Click Update button in order to adapt new value sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group aroeweb
5. 2 3 2 3 1 Construct optimization for expression Optimization analysis This function recommends to the user with optimized RNA structure V Click Optimization on menu Type sequence name Paste RNA or DNA sequence o Note White space will be removed automatically Type position of start codon o Format 10 12 o Note 10 is the start position and 12 is the end position Type position of motifs o Format 10 12 20 25 o Note 10 is the start position and 12 is the end position If there are more than two motifs use a comma as separator Type cut off score o Format 80 90 o The number of motifs and the number of cut off scores should be same o Note 80 is cut off score for the first motif and 90 is cut off score for the second motif If there are more than two cut off scores use a comma as separator Change temperature if default value is not desired Select RNAfold parameters Select report options o Bestdesign will return the first design that meets better than the cut off score It is not an exhaust search for the best design among all possible design o Top 5 designs will return the first five designs that meet better than the cut off score Click Run The result of request comes out depending on the length of sequence and cut off score User can look up the result in the Search menu later Confidential Proprietary Information Page 15 of 20 sanofi pasteur Automation o
6. CGCCGG TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC C GCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG 230 Figure 14 Result of job finished abnormally 2 4 AROE session time out gt Ifa user does nothing for 30 minutes the session will disappear lfauserclicks Logout on menu the session will disappear right away Confidential Proprietary Information Page 20 of 20
7. CTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG 16480 2007 10 24 14 56 33 2007 10 24 16 07 17 0 Terminate Figure 13 Result of ongoing job Confidential Proprietary Information Page 19 of 20 sanofi pasteur The vaccines business of sanofi aventis Group Logout sanofi pasteur gt Click sequence name in pink row to see the result of a job finished anormally sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group Score Optimization Search My Info Logout Detail information of job finished abnormally ter 1 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT TAACTTTAAGAAGGAGATATACATATGAGTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGG TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC CAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG 77 79 48 52 77 79 20 80 10 100 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT T ACTTTAAGAAGGAGABATACABATGEBTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGC
8. e ad 1 2007 10 25 15 22 50 Terminate user1111 1 2007 10 25 15 24 17 Terminate Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 6 Monitoring ongoing jobs Microsoft Internet Explorer Do you really want to terminate this job Cancel Confidential Proprietary Information Page 11 of 20 sanofi pasteur 2 2 RNA structure scoring This function enables a user to see how good the secondary structure of RNA is for given motif s VV ON Y Click Score on menu Paste RNA or DNA sequence in the text box o White space will be removed o Thelength of a given sequence is limited up to 7000 Type position of motifs o Format 10 12 20 25 etc o Note 10 is start position and 12 is end position If there is more than two use a comma as separator Change temperature if default value is not desired Select RNAfold parameters Click Run Click What is score link to learn how the score is calculated Confidential Proprietary Information Page 12 of 20 sanofi pasteur sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group Score Optimization Search My Info Logout Help Predict score for particular motif s of sequence What is score DNA Sequence Size 490 TACATATGAGTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGGTGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTG
9. ential Proprietary Information Page 3 of 20 sanofi pasteur 1 Introduction The AROE Automation of RNA Optimization for Expression web server provides alternative designs for a given RNA or DNA sequence RNA secondary structure is predicted using the Vienna RNA package http tbi univie ac at ivo RNA RNA structure optimization attempts to free interested motifs such as AUG and SD sequence from complicated secondary structures 11 URL Users can navigate the AROE web server by accessing http catorhpc100 8080 Confidential Proprietary Information Page 4 of 20 sanofi pasteur 2 Function list The AROE web server provides the following functions Administration o Registration o User Login o Changing user information o Changing configuration file o Monitoring ongoing jobs gt RNA structure scoring gt Constructing optimization for expression Confidential Proprietary Information Page 5 of 20 sanofi pasteur 21 Administration 2 1 1 Request of registration To navigate AROE web user should register first Click register on Login page gt Type all information gt The length of ID must be 4 AR OE Sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group Score Optimization Search My Info Login Help ID Length is 4 Password Length is up to 20 First Name 0 F Last Name P
10. f RNA Optimization for Expression The vaccines business of sanofi aventis Group demo Score Optimization Search My Info Logout Help Optimize sequence What is score Name of sequence demo prj1 DNA Sequence Size 490 TATACATATGAGTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGGTGCCGGTGAGCAAAGTGGTGAGCACCGATGAAT A TGTGGCGCGTACCAACATTTATTATCATGCGGGCACCAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAA CAACAACAAAATTCTGGTGCCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTT TCCGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCGTGGCCAGCCGCTGGG CGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG Position of start codon 7 9 45 47 Indicate start codon with and Positions of motif 48 52 77 79 i e 20 23 109 113 Indicate motif with and 1 Cut off score 70 80 Range 0 100 i e 80 90 RNAfold parameters Rescale energy parameters temperature 7 tetraloops v no dangling end energies Cno GU pairs at the end of helices Report type Best design with fasta format sequence Top 5 designs with fasta format sequence Email Joe Wanq sanofipasteur com Tel 416 667 2700 ext 3275 Figure 9 Optimization analysis A ROE sanofi pasteur Automation of RNA Optimization for Expression The vaccines business of sanofi aventis Group demo Op
11. hone Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 1 Registration for new users Confidential Proprietary Information Page 6 of 20 sanofi pasteur 2 1 3 Approval of registration Only administrators can access this menu gt Log to AROE with administrator account gt Click Approval on menu gt Check checkbox for approving registration Click Grant button gt Checked users will disappear AR OE Automation of RNA Optimization for Expression aroewebm Approval Configuration List of users waiting for approval All test test sanofi pasteur The vaccines business of sanofi aventis Group Monitoring My Info Logout test aroe sanofipasteur com Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 2 Approval of registration Confidential Proprietary Information Page 7 of 20 sanofi pasteur 2 1 3 Logging on to the system An AROE session must be initiated by logging into the system When presented with the screen below type in your credentials that you have been approved by an administrator gt Type ID and Password gt Click Login pasteur Automation of RNA Optimization for Expression demo Score Optimization Search My Info Logout ID demo Password register Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 3 Login
12. m Approval Configuration Monitoring My Info Logout Help View Update Configuration File Common H directories TomcatDir usr local apache tomcat 5 5 23 root dir of tomcat server ExeDir usr local apache tomcat 5 5 23 bin aroe executable files WVorkDir usr local apache tomcat 5 5 23 webapps aroe work temporary files for local mode CtDir usr local apache tomcat 5 5 23 webapps aroe work ct for saving ct files of good design NfsBinDir big2 home alee aroe bin for RNAfold Cluster E HostName catorhpe100 host name of cluster WorkDir big2 home alee aroe aroe work for ct files for only cluster mode executable file names ExeFiles TranPepExe transeq Tran mbigExe backtranarmbicg lt Email Joe Wang sanofipasteur com Tel 416 667 2700 ext 3275 Figure 5 Changing configuration file Confidential Proprietary Information Page 10 of 20 sanofi pasteur 217 Monitoring ongoing jobs Only administrators can access this menu gt Log into AROE with administrator account Click Monitoring on menu Click Terminate link in order to terminate a job o Click OK button to commit to terminating the job AROE sanofi pasteur Automation of RNA Optimization for Expression minae ans a 4 aroewebm Approval Configuration Monitoring My Info Logout Processing job list ter 4 2007 10 24 14 56 33 Terminate ter 32 2007 10 25 09 10 16 Terminat
13. sanofi pasteur The vaccines business of sanofi aventis Group AROE User Manual Automation of RNA Optimization for Expression Version 1 0 Last modified 14 December 2007 by Alex Lee Confidential Proprietary Information Page 1 of 20 sanofi pasteur Table of Contents List 3 1 Pave OIC PDC 4 1 1 URL Saree 4 2 Euncton cora te LH M 5 2 1 6 2 T4 REQUESUOR TESTS sio eoi eer Stud ets VER EX stead deed pe vo be der Ui 6 2 1 2 Approval of registration 7 2 1 3 of to Ue SVSEGHLS ato 8 2 1 4 Logging out trom the Systemic eee ec o es Se ee 8 2 1 5 Changing user information cis rn ei Ee D nir XY RENS IN EY Fe SE eed 9 2 1 6 Changing configuration soos ossi tn det va ER eo n PING QUO RU ME 10 2 1 7 Monitor ongona 11 22 RNA SUUCEUTG SCOTTI BS Ego e ees urs ost Ete Bel ote ti e 12 2 3 Construct optimization for 51 15 2 3 1 Opiiirzatioi act va E re RERO OM Eat EN 15 2 32
14. timization Search My Info Logout Result for your request Your request is sent to queue You can check the result of your request on Search menu later Figure 10 Optimization analysis reply Confidential Proprietary Information Page 16 of 20 sanofi pasteur 2 3 2 Optimization results This function enables users to view the results of sequence optimization Click Search on menu gt see detail information click a sequence name There are three different status for jobs o Normally finished job coloured white o Abnormally finished job coloured pink o Ongoing job coloured green AR OE Automation of RNA Optimization for Expression sanofi pasteur The vaccines business of sanofi aventis Group Score Optimization Search My Info Logout List of job Abnormal finished pro i 10 90 BEST 2007 11 14 13 36 37 2007 11 14 13 36 42 pro 2 20 90 BEST 2007 11 14 13 48 21 2007 11 14 13 53 57 pro 3 60 90 BEST 2007 11 14 13 50 06 2007 11 16 12 00 36 pro 4 20 90 BEST 2007 11 19 14 05 10 2007 11 19 14 06 01 pro 7 20 90 BEST 2007 11 20 09 27 58 2007 11 20 09 29 43 ro 8 20 90 BEST 2007 11 20 09 37 58 2007 11 20 09 44 22 Figure 11 List of request for optimization Confidential Proprietary Information Page 17 of 20 sanofi pasteur Click sequence name in white row to see the result of a job finished normally Yellow bases are specified motifs
15. ult of job finished normally gt Click CT File link to see ct file for selected design in result screen of the job finished normally Confidential Proprietary Information Page 18 of 20 sanofi pasteur Click sequence name in green row to see the result of an ongoing job Click Terminate link to terminate a job in the result screen of ongoing job demo AROE Automation of RNA Optimization for Expression Score Optimization Search My Info Detail information of on going job status ter 4 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT TAACTTTAAGAAGGAGATATACATATGAGTCTGTGGCTGCCGAGCGAAGCGACCGTTTATCTGCCGCCGG TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC CAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGCCTGCAGTATCGTGTGTTTCGTATTCATCTGCCGGATCCGAACAAATTTGGCTTTC CGGATACCAGCTTTTATAATCCGGATACCCAGCGTCTGGTGTGGGCGTGCGTGGGTGTGGAAGTGGGTCG TGGCCAGCCGCTGGGCGTGGGCATTAGCGGTCATCCGCTGCTGAACAAACTGGATGATACCGAAAACGCG 77 79 48 52 7 7 79 20 80 10 100 CGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTT TGCCGGTGAGCAAAGTGGTGAGCACCGATGAATATGTGGCGCGTACCAACATTTATTATCATGCGGGCAC CAGCCGTCTGCTGGCCGTGGGCCATCCGTATTTTCCGATCAAAAAACCGAACAACAACAAAATTCTGGTG CCGAAAGTGAGCGGC
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