OxyGene User Guide v1.0
Contents
1. Locus Tag Ajs_1958 Pressing then the Go button will result in displaying the replicon window centred on that position The zoom and rotation buttons may further be used to view the replicon and OxyDB instances as desired 4 Contact We hope you will find OxyGene useful and this guide helpful If you have any questions or suggestions feel free to contact us at fhubler univ rennesl fr Of stephane avner univ rennesl fr Thank you The B SIC team Bibliography Stothard amp Wishart 2005 Stothard P Wishart DS Circular genome visualization and exploration using CGView Bioinformatics 21 537 539 Thybert amp al 2008 Thybert D Avner S Lucchetti Miganeh C Cheron A Barloy Hubler F OxyGene an innovative platform to investigate oxidative response genes in prokaryotes whole genomes submitted 2008 OxyDB 2008 B SIC The OxyDB documentation 2008 http www umr6026 univ rennesl fr english home research basic software JGraph www jgraph com2. each tab specifies the genome and replicon in which the instance is found its locus tag its annotation usual name its begin and end positions its annotation confidence level and finally its specific sequence As an exercise one could check that the signature motifs can be found within the sequence 10 OxyGene Gene Description OxyDB Name SOD_CUZ Function Confidence 1 OxyDB Id OXYDB 2 2 Size mean 189 0 sd 42 2 Definition Copper Zinc SOD Signature s x1 M2 M2 3 with Mi Motif DN x 3 D x x 2 3 G G G G x RE x 2 C G ILVMT IVWGA M2 Motif GP G FLY YH G LVMIF HQ IVE H x 2 PA x C DE M3 Motif VIIM IVL EYT x 3 TV QD x 2 3 QNDFY AS x GE NMAGDEK AS GD x 4 CLOV EC number s 1 15 1 1 Typical Reaction s 2 O7 2 H gt H202 Oz Description Enzymes of this class show superoxide dismutase activity they detoxify two superoxide anions into dioxygen and hydrogen peroxide Ref 1 Ref 2 The SOD_CUZ class includes the bacterial copper zinc SOD family sequences This family is phylogenetically related to the eucaryotic cytoplasmic copper zinc family These SOD use Copper and Zinc as cofactors to perform the superoxide dismutase acivity This class of SOD is found in the periplasm among the gram bacteria and among the Mycobacterium group This class of SOD is associated to the
3. 3 2 Acel_0566 597796 597389 1 YP_872325 1 Acel_0566 Figure 9 The Genes Table Q Pal ca OxyGene Version 1 0 5 10 A CRG zoi Knowledge Input Tables Sequences Maps Localisation R ry A y Genome All submitted Genomes Ea Proteic Nucleic Acids Save as Fasta file Gene SOD_FMN A v Genome OxyDBName OxyDB Id Acidobacteria bacterium Ellin345 SOD_FMN OXYDB 2 1 Acidovorax avenae subsp citrulli AAC SOD_FMN OXYDB 2 1 Acidovorax avenae subsp citrulli AAC SOD_FMN OXYDB 2 1 Acidovorax sp JS42 SOD_FMN OXYDB 2 1 Acinetobacter baumannii AYE SOD_FMN OXYDB 2 1 Acinetobacter baumannii ATCC 17978 SOD_FMN OXYDB 2 1 Gene Name Locus Tag Sequence Acid345_3693 MAHEVPPLPYDYSALEPTIDT QTMHLHHDKHHLAYVTNLNA Aave_2568 MEHTLPPLPYAIDALAPHYSQETLEYHHGKHHNAYVYNLNN Aave_2662 MPHTLPALPYAYDALEPHIDARTMEIHHTKHHQTYVNNLNA Ajs_2301 MEHTLPPLPYAIDALAPHYSQETLEYHHGKHHNAYVYNLNN sodB ABAYE1134 MTTITLPALPYGYDDLAPHISKETLEYHHDKHHNTYVVNLN A1S_2343 MYNPANARNRNMTTITLPALPYGYDDLAPHISKETLEYHHD allows the biologist to easily reassemble in a fasta file the sequences of the desired genes To do so using the Genome Gene selection panel Genome Brucella_abortus_9 941 ES Gene All Genes found is A v 12 OxyGene the biologist must choose the desired genome or may choose all genomes altogether then one of the OxyDB genes that exist in the selected genome or all its OxyDB gene
4. OxyDBGenes Reference Subsystems Detoxification E v J OXYDB 1 Catalase OxyDB Name CAT_MNG Function Confidence 1 7 OXYDB 1 1 Monofunctionnal OXYDB 1 1 1 Catalase monofonctionnal typical CAT _MON OXYDB 1 1 2 Catalase GATase CAT_GAT Definition Manganese Catalase OXYDB 1 1 3 Catalase SrpA related CAT_SRP OXYDB 1 2 Bifunctionnal Catalase CAT_BFL OXYDB 1 3 Manganese Catalase CAT_MNG gt OXYDB 2 Superoxide dismutase gt OXYDB 3 Peroxidase gt OXYDB 4 Nitric oxide Dioxygenase gt OXYDB 5 Nitric oxide reductase gt OXYDB 6 Superoxide reductase EC number s OxyDB Id OXYDB 1 3 Size mean 260 4 sd 58 8 Signature s 5 with 1 11 1 6 Typical Reaction s 2 H202 gt 2 H20 Oz Description molecules of hydrogen peroxide by producing two molecules of water and one of dioxygen Ref 1 Ref 2 The CAT_MNG class belongs to the manganese catalase family also referred to as pseudocatalase This catalase family does not contain heme and instead uses manganese as a cofactor to catalyse the catalatic reaction The CAT_MNG family has a specificity activity lower than other kinds of catalases Ref 3 This class also includes the cotJC protein which is a constituent of the inner 4 layers of the bacillus subtilis spore coat Ref 4 M References Ref 1 Pubmed 11260470 Ref 2 Pubmed 4084532 a Ref 3 Pubmed 14745498 v
5. Proteic Nucleic Acids All sequences displayed in the table may be saved into a fasta file by clicking on the Save as Fasta File button Seas Fastafile then selecting the repertory and defining the file name For example the sequences shown above would be saved thus choose different genomes same OxyDB gt BruAbl_0588 Brucella_abortus_9 941 SOD_FMN MAFELPALPYDYDALAPFMSRETLEYHHDKHHQAYVTNGNKLLEGSGLEGKS FEEIVKES FGKNQALFNNAGOHYNHI HFWKWMKKDGGGKKLPGKLEKAFD SDLGGY DKFRADF IAAGAGOFGSGWAWLSVKDGKLEISKTPNGENPLVHGAAPTLGVDVWEHSYYIDYRNARPKYLEAFVDSLVNWDYVLEMYEKAA gt BruAbl 0933 Brucella_abortus_9 941 PRX_BCP MAHPQVGDMAPDFTLPSDHGEITLSSLKGHPVVVYFY PKDDTSGCTREATAFSQLKAEFDRIGVRVIGLS PDSATKHARFRTKHALTVDLVADEDRVALEAY GVWVEKSMYGRKYMGVERTTFLIGADGRIAQVWNKVKVDGHAQAVLEAARRL gt BruAb2_0827 Brucella_abortus_9 941 CAT MON MTDRPIMTTSAGAPI PDNONSLTAGERGPI LMQDYQLIEKLSHONRERI PERAVHAKGWGAYGTLTITGDISRYTKAKVLOPGAQT PMLARFSTVAGELGAA DAERDVRGFALKFY TOQEGNWDLVGNNTPVFFVRDPLKFPDFIHTOKRHPRTHLRSATAMWDFWSLS PESLHOVTILMSDRGLPTDVRHINGYGSHTYSFWND AGERYWVKFHFKTMOGHKHWTNABFAEOVIGRTRESTOQEDLFSAIENGEFPKWKVOVOIMPELDADKT PYNPFDLTKVWPHADY PPIDIGVMELNRNPENYFT EVENAAFS PSNIVPGIGFS PDKMLQARTFS YADAHRHRLGTHYES I PVNOPKCPVHHYHRDGOMNVYGGIKTGNPDAYYEPNSFNGPVEQPSAKEPPLCISG NADRYNHRIGNDDYSOPRALFNLFDAAOQKORLFSNIAAAMKGV PGF IVEROLGHFKLIHPEYEAGVRKALKDAHGYDANTIALNEKITAAE gt BruAb2_ 0930 Brucella_abortus_9 941 NOR_BSH MKYQSQKVAMLY FYGALALFVAQVLFGVVAGTIYVLPNTLSVLLPFNIVRMIHTNALIVWLLMGFMGSTYYLLPEETETELY
6. Table button and specifying a repertory and name for the file These files may ultimately be opened using Microsoft Excel or your favourite text editor Clicking on a coloured item intersection of an OxyDB gene column and genome row produces the opening of a new window which provides detailed information to the biologist see Figure 8 The upper part of this window is the description of the OxyDB gene c ass similar to that displayed in the OxyDB ontology of the Knowledge tab The information provided in this part of the window is common to all instances This part defines the OxyDB gene class and remains identical in the whole OxyDB column specifying the OxyDB number OxyDB name corresponding EC numbers function confidence level its signature motifs and providing a short description of the gene together with some references and links to related web sites The Function Confidence Level is attached to the OxyDB class and represents the degree to which its function may be trusted Its semantics again see hybert et al 2008 is the following 3 The enzymatic activity has been defined 7 vitro or in vivo The mutant phenotype suggested the gene function 1 No function is defined but its phylogenetic group is close to an OxyDB class whose confidence level is 2 or 3 The lower part enumerates the different mstances of the OxyDB gene class in the considered genome A different tab is created here for every instance of the gene
7. basic software In order to run OxyGene needs Java JRE 5 or a more recent version If not already installed on your machine the latter can be downloaded at the following address http java sun com javase downloads index jdk5 jsp Once OxyGene has been downloaded unzip the OxyGene zip or OxyGene tar gz file by clicking on it or by typing under Linux tar xzvf OxyGene tar gz An oxyGene directory should appear In order to launch OxyGene no matter which platform first go to the oxyGene directory On Windows simply double click on file oxycene bat On Mac OS X double click on file oxyGene command On Linux double click on file oxycene sh of in a terminal window type oxyGene Depending on the requests submitted the OxyGene Client may require large amounts of memory By default this is somewhat accounted for within the files above However if your computer has less than 1Go available RAM please replace the xmxig option inside the above corresponding file by xmx128m xmx256m Of Xmx512m according to your system available RAM The application OxyGene launches after a few seconds you should see the following window appeat r e208 eI OxyGene Version 1 0 5 Lo d Z Search subsystem Detoxification B D by Genome D by Gene Figure 1 The Input tab at the beginning 3 Description Demonstration of the Application At the beginning two different tabs appear in the OxyGene window The Knowledge ta
8. genes are effectively present in these genomes with their properties locus tag begin end positions confidence levels sequence etc Once the data has returned from the server the OxyGene client Window switches to present a table showing the presence or absence the number of paralogs rather of all OxyDB genes in the selected genomes Figure 4 B OxyGene Version 1 0 5_ Ss Fs Knowledge Input Tables Sequences Maps Localisation Genomes Table Genes Table View Number of Paralogs D Annotation Score Phylum Level 2 Save Table Genome Phylum CAT MON CAT_GAT CAT_SRP CAT_BFL CAT MNG SOD_FMN SOD_CUZ SOD_NKL OHR_OHR OHR_OSM OHR_LKE HPX_HPX a Acidobacteria bacterium Ellin345 Acidobacteriales te Acidothermus cellulolyticus 11B Actinobacteridae 1 2 Acidovorax avenae subsp citrulli AACOO Betaproteobacteria 1 1 Acidovorax sp JS42 Betaproteobacteria 1 Acinetobacter baumannii AYE Gammaproteobacteria 0 o Acinetobacter baumannii ATCC 17978 Gammaproteobacteria 1 ter ROO HKRroOooOo KRrOoROK RR RINIOF 0 o 2 1 1 1 oooocoom oooomo Kee ROO CORRE Hee ROR moooo Figure 4 Submission of the chosen genomes to OxyGene results in the Number of Paralogs Table It can be seen that in addition to the Knowledge and Input tabs new tabs have been included in the OxyGene client window A Tables tab showing different tables with lots of information see Section 4 3 A Sequences
9. membrane and this seems to be the case for all the gram bacteria Ref 3 SOD of Haemophilus ducreyi seem to include heme binding poperties Ref 4 References Ref 1 Pubmed 1938942 P Ref 2 Pubmed 17704897 a Ref 3 Pubmed 11563965 M Search occurences in all sequenced genomes Genome Brucella melitensis biovar Abortus 2308 Function Confidence 1 Replicon NC_007624 Begin Position 534069 Annotation Score fi Locus Tag BAB2_0535 End Position 534590 NCBI Link YP_418725 1 Gene Name sodC Frame B KEGG Link BAB2_0535 Sequence atgaagtccttatttattgcatcgacaatggtgcttatggcttttccggctttcgcagaaagcacgacggtaaaaatgtatgaggcgctgccgacc O Proteic ggaccgggtaaagaagttggcaccgtgatcatttccgaagcecccgggcgggctgcacttcaaggtgaatatggaaaagctgacgccgggcta Nucleic catggctttcatgttcacgaaaatccaagctgcgctccgggagaaaaagacggcaagatcgtaccggctcttgctgccggcgggcattatgat ccgggtaatacccatcaccatttaggacctgaaggtgatggacatatgggcgatttgccacgcctgagcgccaatgctgacggcaaggtgagt gaaaccgttgtcgctccacatctcaagaaattggcggaaatcaagcagcagttctttgatggtccatgtcggaggggataattattccgataagcc tgagccgcttggtggcggtggtgcccagttttgcctgcggcgtgatcgaataa Figure 8 OxyDB gene description window showing the OxyDB gene class in its upper part and the particular instances under different tabs in the lower part From this window it is also possible to search for all occurrences of this OxyDB gene class in all sequenced bacterial genomes Just click on the S lt 5 button on the up
10. tab enabling the retrieval of all actual sequences of all OxyDB gene instances of all selected genomes A Maps tab showing the subsystem e g detoxification for each selected bacterial genome this subsystem will be a subset of the reference subsystem A Localisation tab enabling the representation of the location of each OxyDB gene on all replicons of all selected genomes All these tabs will be described in details in Sections 3 3 to 3 6 3 2 2 Search by Gene The bio analyst can investigate all genomes that possess a particular OxyDB gene or a combination of these by clicking on the Search by Gene radio button seach by Genome _O byGene A new input interface then appears in the Input tab The OxyDB ontology appears on the left hand side of the window The biologist may now select one or more OxyDB genes and ask OxyGene to produce the list of genomes that contains at least one of those genes This is achieved by clicking on the rt Genomes containing Selected Gene button As a result the window presents the corresponding genomes i e those with at least one selected OxyDB gene present in alphabetical order in the upper list box and the remaining genome names in the lower one see Figure 5 By default the corresponding genomes are selected and the remaining ones are not It is possible to save the two lists in a text file txt by clicking on the save button above the lists User Guide 7 eee gl
11. tab to view a new replicon is achieved by clicking on the button at the top of the client window on the left or right side depending on where one wants to add the viewing tab Likewise clicking on the dustbin button removes the corresponding current viewing tab Inside the tab the biologist must use the control panel Genome Acidobacteria bacterium Ellin345 HH Replicon NC_008009 xs M Zoom Move SPSS O Position kb Genes RBR_RBR A PRX_AHP t Locus Tag id 345_4781 Legend Go gt G Whole CG View Save as JPeg User Guide 19 in order to display the desired replicon or zoomed part of the replicon The Genome combo box at the top allows the user to select the desired genome the Rep icon combo box underneath allows the selection of the replicon The list of the OxyDB genes present within that replicon appears in the list box The Legend field allows the biologist to add some commentary which will be placed at the bottom of the figure Clicking then on the Whole CG View button will generate the drawing of the whole selected replicon with all the OxyDB genes associated The CG View then shows the whole circular replicon with its name and size in the middle its genome name at the top left corner the positions in kbp kilo base pair on the circular replicon and finally the OxyDB genes drawn on their strand forward in green and reverse in red at their correct positions and with exact lengths T
12. OxyGene User Guide v o B SIC UMR 6026 June 2008 1 Introduction 1 1 Objectives OxyGene is a Client Server application which aims at constructing the sub systems of the genes involved in oxidative stress for all sequenced bacterial genomes The sequences of the oxidative stress genes identified from the literature were aligned and analysed so as to establish a set of signatures stored in a database called OxyDB A novel ontology of the genes of detoxification based upon the set of signatures is proposed in OxyGene and enriches the existing ontology by being more precise The repertories for all sequenced bacterial genomes are then obtained using the OxyGene Annotator from strict pattern matching between the genomes and the genes signatures A Graphical User Interface presented in this guide has been developed to ease the query and bioanalysis processes 1 2 Graphical User Interface GUI Not only does OxyGene supply the subsystems of oxidative stress genes but it also seeks to facilitate the job of the biologist or bioanalyst by providing a certain number of potentialities such as Investigate the presence or absence of the oxidative stress OxyDB genes within the chosen sequenced genomes Enumerate the sequenced genomes that possess an instance of a given oxidative stress gene View and save under fasta format all nucleic and proteic sequences of any such gene of any chosen genome View and save tables sh
13. OxyGene Version 1 0 5 f oN Knowledge Input Search subsystem Detoxification By by Genome by Gene Gene Selection Genes involved in subsystem Genomes with All Selected Genes At least one Selected Gene He LF Detoxification Present O by Phylogeny v 1 e Bon ee a el so Acaryochloris marina MBIC11017 0 1 1 Monofunctionna Acidiphilium cryptum JF 5 OXYDB 1 2 Bifunctionnal Catalase CAT_BFL _ OXYDB 1 3 Manganese Catalase CAT_MNG gt OXYDB 2 Superoxide dismutase Acidobacteria bacterium Ellin345 Acidovorax avenae subsp citrulli AACOO 1 Acinetobacter baumannii AYE gt OXYDB 3 Peroxidase Acinetobacter baumannii ATCC 17978 gt OXYDB 4 Nitric oxide Dioxygenase Aeromonas salmonicida subsp salmonicida A449 2 gt OXYDB 5 Nitric oxide reductase Agrobacterium tumefaciens str c58 X gt OXYDB 6 Superoxide reductase Remaining Genomes Acholeplasma laidlawil PG 8A 0 Acidothermus cellulolyticus 11B Acidovorax sp JS42 Acinetobacter baumannii SDF Acinetobacter sp ADP1 Actinobacillus pleuropneumoniae L20 Actinobacillus pleuropneumoniae serovar 3 str JLO3 p Actinobacillus succinogenes 130Z Find Genomes containing Selected Gene s C Process Selected Genomes J Figure 5 The resulting window when an OxyDB gene is selected and the Find Genomes button pressed The biologist may then select unsele
14. Rhodospirillales v L Acetobacteraceae Y Acidiphilium Acidiphilium_cryptum_JF 5 Y Gluconobacter Gluconobacter_oxydans_621H v Cranulihactar Click on the Add button A to add the selected genomes to the Chosen Genomes list box Chosen Genomes T Brucella_abortus_9 941 Brucella_melitensis Brucella_melitensis_biovar_Abortus Brucella_ovis Brucella_suis_1330 Genomes may be removed from this list box by selecting them and clicking on the T button A group of genomes containing all present genome names may also be defined here by clicking on the Create new Q group of genomes button a new editable field will appear 57er Croup Name simply enter a name for this new group of genomes and press Enzer the group will be added to the Group of genomes combo box Online Genomes on the left hand side and may later be used to retrieve the selected genomes easily Once all the genomes to be analysed with respect to the oxidative stress repertory are imported in the list box Chosen genomes the biologist may submit the request to OxyGene This is performed by clicking on the Determine Genes involved in Chosen Genomes button The OxyGene server then receives the request reads it recognizes the submitted names of the pre computed genomes and returns to the client the desired 6 OxyGene data The latter contains all the information regarding the selected genomes response to oxidative stress i e which OxyDB
15. STKLAVIQFWLFFVAAGVAV AGYLFHIHEGREFLEQPFFIKVGIVVVCLIFLFNITLTALKGRKTTVINILLFGLWGLALFFLFAFYNPINLALDKLYWWYVIHLWVEGVWELIMASILAFL MIKLNGIDREVVEKWLYVIVGLALFSGILGTGHHYYWIGAPGYWQWIGSLFSTLEVAPFFTMVMFTFVMTWRAGREHPNRAALLWS IGCSVMAFFGAGVWGF LHTLSSVNYYTHGTOLTAAHGHLAFFGAYVMLNLAAMAYAT PETRGRTPYNQWLSMVS FWMMCTAMSVMTFALTFAGVVOQVHLORVLGENFMEVOQDOLALFY WIRLGSGVVVVISALMFVWAVLVPGRORSOKLSGFAQQPAE gt BruAb2_0335 Brucella_abortus_9 941 GLB_ TRC MTILINOQPHPSIDRDSIDRLVEIFYGRAREDEIIGPIFNRTVKDWDHHLARISEFWSSVILKTGGY DGRPMPPHLALNLENEHFDLWLELFEQTAQEIFPPE AATIFVDRARRIADSFEMATATHSGRIRAPRHSRLPLIS gt BruAb2_0347 Brucella_abortus_9 941 OHR_OHR MPILYTTOSTATGGRTGSAKTADGRLSVVLDT PKELGGQGGEGTNPEQLFASGYAACFLGALKFAAAKEKISIPAESTVTATVGIGPREDGTGFGLDVALSI ALPGIDKAKAEELVQAAHIVCPYSHATRGNLDVRLSVA gt BruAb2_0527 Brucella_abortus_9 941 SOD_CUZ MKSLFIASTMVLMAFPAFAESTTVKMYEALPTGPGKEVGTVVISEAPGGLHFKVNMEKLTPGYHGFHVHENPSCAPGEKDGKIVPALAAGGHY DPGNTHHHL GPEGDGHMGDLPRLSANADGKVSETVVAPHLKKLAEIKORS LMVHVGGDNYSDKPEPLGGGGARFACGVIE gt BruAb2_0522 Brucella_abortus_9 941 PRX_AHP MLGIGDKLPSFKVTGVKPGFNHHEENGVSAFEEVTEQSFPGKWKVIFFY PKDFTFVCPTETAEFARLASEFEDRDAVVLGGSTDNEFVKLAWRRDHKDLNKL PIWSFADTNGSLVDGLGVRS PDGVAYRYTFVVDPDNVIQHVYATNLNVGRAPKDTLRVLDALOQTDELCPCNREVGGETLKAA User Guide 13 3 5 The Maps tab The Maps tab allows the biologist to view the subsystem e g detoxificatio
16. Search occurences in all sequenced genomes Figure 2 OxyDB genes ontology and characteristics of each OxyDB gene OxyGene aey OxyGene Version 1 0 5 a Genomes OxyDB Genes Reference Subsystems Detoxification Compain Detoxification map io Symbol OxyGene B SIC UMRE026 2008 Name D_FMN f z O S e ee sa A Fi R_DFX f N T_MON CAT_GAT CAT_SRP lcat CAT MNG O moe aa Je or H0 HPX HPX HPX_VAN OHR OSM OHR_LKE GsH_PRX CAT BFL CCP_CCP PRX_1CY prxane PRx 8cP prxanp PRX_TPX R_RBR RBR_RPR peR_suL RBR RRC RBR_LKE kl H 0 PRX icy PRXAHE PRX8CP PRX_AHP PRX_TPX OHR_OHR OHR_OSM OHR_LKE GSH_PRX B R OOH R OH SH_PRX _ oR se ONOOH NO7 INOR_NRF gt u s mp fete sci NH j fcup_tRP c 8 TRN CLB_TRO s E Ci NOR_BLG Nox n NOR BSH NORFBR NOR_Fex gt a N20 Figure 3 Detoxification reference sub system showing all known detoxification potentialities of all sequenced bacteria 3 2 The Input Tab The Input tab already shown in Figure 1 allows the biologist to express its request The subsystem detoxification reparation reduction regulation etc must first be selected only detoxification is available for the time being Reference Pathway Detoxification E t Then the biologist may sub
17. able Genome Phylum Replicon OxyDB Name OxyDBid Annotat Score Gene Name Locus Tag Begin End Frame NCBI KEGG Acidobacteria bacterium Ellin345 Bacteria NC008009 NOR_BLG OXYDB 5 3 2 2 Acid345_0364 405282 402997 1 YP_589443 1 Acid345_0364 SOD_FMN OXYDB 2 1 2 Acid345_3693 4369001 4369612 2 YP_592768 1 Acid345_3693 CAT_BFL OXYDB 1 2 2 Acid345_1356 1645812 1648070 S YP_590432 1 Acid345_1356 CAT_MNG OXYDB 1 3 2 Acid345_1673 2025480 2026313 3 YP_590748 1 Acid345_1673 RBR_RBR OXYDB 3 4 1 2 Acid345_2736 3237650 3238204 2 yP_591811 1 Acid345_2736 PRX_AHP OXYDB 3 5 1 2 Acid345_4100 4859937 4860473 3 YP_593174 1 Acid345_4100 PRX_AHE OXYDB 3 5 3 2 2 Acid345_4781 5648665 5648321 3 YP_593854 1 Acid345_4781 PRX_BCP OXYDB 3 5 3 3 2 Acid345_2815 3339273 3339794 3 YP_591890 1 Acid345_2815 PRX_BCP OXYDB 3 5 3 3 3 pseudogene 5576485 5576021 3 GSH_PRX OXYDB 3 2 2 Acid345_1872 2252507 2252986 2 YP_590947 1 Acid345_1872 HPX_HPX OXYDB 3 3 1 2 Acid345_3581 4231917 4232738 3 YP_592656 1 Acid345_3581 HPX_HPX OXYDB 3 3 1 2 Acid345_3102 3686495 3687325 2 YP_592177 1 Acid345_3102 HPX_HPX OXYDB 3 3 1 2 Acid345_3745 4419069 4419911 3 YP_592819 1 Acid345_3745 OHR_OSM OXYDB 3 1 2 2 Acid345_0303 324176 324598 2 YP_589382 1 Acid345_0303 OHR_LKE OXYDB 3 1 3 2 Acid345_1947 2341327 2340845 3 YP_591022 1 Acid345_1947 Acidothermus cellulolyticus 11B Bacteria NC_008578 GLB_TRO OXYDB 4 1 3 2 4 Acel_1609 1810627 1811025 1 YP_873367 1 Acel_1609 SOD_NKL OXYDB 2
18. ame annotation confidence level i e 2 The semantics of the Annotation Confidence Level see Thybert et al 2008 is the following 3 The gene expression of this particular instance of the OxyDB gene has been experimentally verified i e protein or RNA effectively expressed 2 This particular instance of the gene belongs to an OxyDB group that contains at least one experimentally verified expressed gene 1 This particular instance of the OxyDB gene seems to be ill formed i e a pseudogene frameshift or fragment User Guide 9 The second column of the different tables is devoted to providing Phylum information the biologist needs only specify the phylum level he she wants to include in the table This is achieved by selecting the appropriate level on the spin box widget Y Level 28 It is possible to change the fundamental colour from which all the shades are derived either for the number of paralogs colour or the annotation confidence level colour by clicking on the colour button next to the corresponding radio button A colour definition window will then open Cones e e Please select gene color HSB RVB aa a Dernier HH a Aper u Go oO HB Echantillon de texte Echantillon de texte Ba BB conection de texte echantilion de texte Echantillon de texte Echantillon de texte 0K Annuler Restaurer Both tables can be saved as txt or xls files by clicking on the Sae
19. b which gives the a priori knowledge upon which OxyGene is based The Input tab which enables the biologist to express its request User Guide 3 3 1 The Knowledge Tab The Knowledge tab exhibits the a priori knowledge of OxyGene represented in three sub tabs a the taxonomy of genomes imported from Genbank b our OxyDB ontology of the oxidative stress genes Figure 2 c the reference subsystems which show all possible paths involved in oxidative stress used by all bacteria with the OxyDB genes involved in each path Figure 3 The OxyDB genes are denoted by two identifiers an OxyDB number which draws inspiration while being different from the nomenclature of Margaret Riley and an OxyDB name e g CAT_GAT that stands for mono functional catalase with Gatase domain which we found were necessary to denominate the OxyDB genes in a more eloquent or expressive manner For further details please see the OxyDB documentation OxyDB 2008 These three sub tabs present some information for reference purposes allowing the bio analyst to answer such questions as is our bacteria pre computed in this OxyGene version What is the OxyGene ontology What are the reference subsystems i e subsystems representing all enzymatic potentialities of all sequenced bacteria of each domain of oxidative stress These three sub tabs are in no way intended to respond to user commands gl ji OxyGene Version 1 0 5 Lo g j Genomes
20. client window Maps mapOO1 Reference Pathway map002 Brucella_abortus_9 941 map003 Brucella_melitensis map004 Brucella_melitensis_biovar_Abortus map005 Brucella_ovis mapOO6 Brucella_suis_1330 the biologist triggers the appearance of the corresponding map on the right hand side aey OxyGene Version 1 0 5 G Knowledge Input Tables Sequences Maps Localisation Representation Comparison _ Remove Map Save as JPeg View Annotation Score H3 map001 Detoxification Subsystem Reference map015 Acidobacteria bacterium Ellin345 Annotation Ey Function Detoxification map Acidobacteria bacterium Ellin345 Published il OxyGene B SIC UMR6026 2008 f gt a Homology 2 2 A 0 Hint 3 f ji 7 A Absence 0 Presence 1 a x or H0 y Font Color mm C Compound Symbol Name M Show Grayed Reference FERRER gt u Maps no map001 Detoxification Subsystem Reference map015 Acidobacteria bacterium Ellin345 z pues ja map016 Acidothermus cellulolyticus 118 R OOH R OH map017 Acidovorax avenae subsp citrulli AACOO map018 Acidovorax sp JS42 H_PRX PRCAHP map019 Delftia acidovorans SPH 1 ea gt u map020 Lactobacillus acidophilus NCFM ONOOH NO7 map021 Sulfolobus acidocaldarius DSM 639 map022 Thermoplasma acidophilum DSM 1728 wo NOR BLG gt u N20 The map above represents the detoxif
21. ct genomes in the standard manner from the two list boxes OxyGene may then be asked to process the selected genomes by clicking on the button Process Selected Genomes THis will send the request to OxyGene as usual and will result in the appearance of the Tables Sequences Maps and Localisation tabs in the client window as in Figure 4 representing all the information gathered on those selected genomes Finally the radio button by Phylogeny bY Phylogeny at the top right corner of the two lists enables the biologist to select unselect the genome names with respect to phylogenetic families Present O by Organism 47 Bacteria 0 Y L Proteobacteria Y Alphaproteobacteria Y Rhodospirillales 2 v L Acetobacteraceae 7 Remaining Genomes Y L Desulfurococcaceae 0 V Aeropyrum Aeropyrum_pernix Y L Staphylothermus T Staphylothermus_marinus_F1 Process Selected Genomes 8 OxyGene 3 3 The Tables Tab Once some genome names have been selected sent to the OxyGene server and processed the client receives the available information from the server and displays it in tables shown in the Tables tab of the client window There are two kinds of tables the Genomes table and the Genes table 3 3 1 The Genomes Table The first table shown is the Genomes Table which by default displays the Number of Paralogs table presenting the number of paralogs for each OxyDB gene for every submitted genome see Figu
22. d by the University of Alberta Canada The reference article is Stothard amp Wishart 2005 and the web site is nttp wishart biology ualberta ca cgview This tab is composed of two viewing frames in order to allow the comparison between different replicons Let us take the example the two bacteria Acidivorax bacterium Ellin345 and Acidothermus cellulolyticus 11B aey OxyGene Version 1 0 5 ons f Knowledge Input Tables Sequences Maps Localisation Ce SP i Acidobacteria bacterium Ellin345 NC_008009 Acidothermus cellulolyticus 118 NC_008578 Genome Acidobacteria bacterium Ellin345 i Genome Acidothermus cellulolyticus 118 HJ Replicon NC_008009 ix Zoom Move Replicon NC_008S Zoom Move Pence PRX_AHE Position kb cones CLB TRO Position kb Laas ana Locus Tag id345_4781 OD NEE O Locus Tag Legend P e C60 gt Legend o gt G Whole CG View A A Save as JPeg __G Whole CG View _ Save as JPeg CAT_MON Acel_2094 OHR_OSM Acid345_0303 PRX_AHE Acid345_4781 PRX BCP Acel_1682 _ PRX_BCP pseudogene 400 kbp NC_008578 2443540 bp GLB_TRO Acel_1609 _ ae OHR_OSM Acel_1608 7 V 1800 kbp NOR_BLG Acid345_0364 rae 1600 kbp The figures produced may help show how similar or dissimilar two bacteria or strains can be with regard to replicon localisation of detoxification genes oP Adding a new
23. enes for all submitted genomes in a single table with different colours to indicate the annotation confidence levels associated to each particular instance of an OxyDB gene is amp amp Gi g OxyGene Version 1 0 5_ Knowledge Input Tables Sequences Maps Localisation Genomes Table Genes Table View Number of Paralogs WE Annotation Score Phylum Level CH Save Table Genome Phylum CAT_MON CAT_GAT CAT_SRP CAT_BFL CAT_MNG SOD_FMN SOD_CUZ SOD_NKL OHR_OHR OHR_OSM Brucella abortus biovar 1 str 9 941 Alphaproteobacteria o o 0 0 BruAb1_0588 o BruAb2_0347 0 a Brucella canis ATCC 23365 Alphaproteobacteria BCAN_BO358 0 o 0 o BCAN_A0S79 ty BCAN B0903 0 2 Brucella melitensis 16M Alphaproteobacteria BMEIIO893 0 o o o BMEI1367 BMEII0581 0 BMEII0409 0 Brucella melitensis biovar Abortus 2308 Alphaproteobacteria BAB2JOB48 0 0 0 0 BAB1_0591 BAB2_0535 0 BAB2_0351 o 3 Brucella ovis ATCC 25840 Alphaproteobacteria BOWJAO322 0 0 0 0 BOV_0567 BOV A0659 0 BOV_A0829 0 0 Brucella suis 1330 Alphaproteobacteria BRAO355 0 o 0 o BR0566 BRA0703 0 BRA0885 o Brucella suis ATCC 23445 Alphaproteobacteria 0 0 0 o BSUIS_AO594 BSUIS_B0688 0 BSUIS_B0877 0 4 Figure 7 The Annotation Confidence Levels table shows all instances of all OxyDB genes for all submitted genomes identifying them by their locus tag and representing their annotation confidence levels by different shades of the same colour here all instances of the genes have the s
24. grams JGraph 16 OxyGene gj Ay OxyGene Version 1 0 5 r Knowledge Input Tables Sequences Maps Localisation C Representation Comparison Remove Map Save as JPeg View _Number of Paralogs B map001 Detoxification Subsystem Reference map002 Acidobacteria bacterium Ellin345 Nb Paralogs Function Detoxification map Acidobacteria bacterium Ellin345 Bal OxyGene B SIC UMR6026 2008 foo Fan D_FMN gt a Ao Ao 1 Ff f Absence O Presence 1 ar f o gt is Font Color X Compound Symbol Name i Show Grayed Reference gt u Map Ko map001 Detoxification Subsystem Reference map002 Acidobacteria bacterium Ellin345 gt u map003 Acidothermus cellulolyticus 11B R OH map004 Acidovorax avenae subsp citrulli AACOO map005 Acidovorax sp JS42 GSH_PRX Pecar map006 Acinetobacter baumannii AYE ae ae gt u map007 Acinetobacter baumannii ATCC 17978 ONOOH NO7 s NO foRBic INOR_BLG Me f gt u N 0 Figure 10 Map of Acidobactereria bacterium Ellin345 representing the number of paralogs of each OxyDB gene class within its genome using different shades of the same red colour 3 5 2 Comparing and combining Maps The OxyGene Client also allows the biologist to compare potentialities among organisms by combining their associated maps Possible combinations are Intersection of any n
25. he labels used to identify the genes include the OxyDB name and locus tag Save as JPeg The image drawn may be saved under jpeg form by clicking on the Save as Jpeg button It is possible to zoom onto a particular position expressed in kb or onto a particular instance of OxyDB gene by using the Zoom Move panel on the right hand side of the control panel To zoom onto a particular instance of an OxyDB gene just click on the corresponding OxyDB name in the list box on the left The Locus Tag radio button will get selected and the corresponding locus tag will be displayed in the associated editable field gt Position kb _ Locus Tag Ajs_1958 Go gt Just press the instance e g button then to display the CG View of the replicon centred onto that particular Acidovorax J542 NC008782 GLB_HMP Ajs_1895 CAT_MON Ajs_1958 1900 kb 2300kbp 2200 2200 kbp PE a E so Then clicking on the zoom buttons allows the bio analyst to zoom respectively further inside or further away the replicon window still being centred on the selected gene locus tag It is also possible to slightly rotate the replicon window press the buttons to respectively rotate the window anticlockwise and clockwise Finally use the Posztion radio button and associated editable field to centre the replicon window onto a particular position expressed in kbp 20 OxyGene Position kb 2200
26. ication capabilities of the Acidobacteria bacterium Ellin 345 bacteria showing the enzymes whose corresponding genes are present within its genome and displaying how they are used along the detoxification paths In this case for instance the enzyme sop_run if expressed may be used to detoxify the Swperoxide compound into Oxygen and Hydrogen Peroxide the latter being in turn detoxified by car_mne into Oxygen and Water or by HPx_HPx ot oxR_osm into Water alone The map above shows the greyed reference map underneath this is obtained by checking the Show Grayed Reference check box E Show Grayed Reference and represents them using their chemical symbol rather than displaying their compound name this effect is obtained by checking the appropriate Symbol Name tadio button Symbol O Name The different colours used to draw the arrows represent different kinds of detoxification paths The colour background of the enzymes corresponds to the annotation confidence level as defined in the legend displayed on the Representation tab on the upper left side of the client window User Guide 15 View Annotation Confidence HA Annotation Function Published Bi B Homology 2 2 Hint 1 E Absence 0 Presence 1 Font Color Compound Symbol Name _ Show Grayed Reference It is possible to change the font colour and the fundamental colour from which the different shades are derived by clicking on the corresponding small bu
27. indow a Representation Comparison panel just above which will be described later and finally a large frame on the right hand side actually showing the map Note that the subsystem for a particular genome is a subset of the reference subsystem which displays all enzymatic potentialities of all sequenced genomes within that oxidative stress domain The reference subsystem is also stored as map001 and is already loaded as a sub tab It is the same reference subsystem as the one proposed in the Knowledge tab The reference subsystem may also be shown on top of each specific bacteria subsystem representing the absent genes and paths by checking the Sow Grayed Reference check box M Show Grayed Reference The OxyGene Client provides another interesting functionality viz the ability to construct new maps by combining old ones the available operators are the intersection N and union U between any number of maps and the difference 6 between two maps Thus it is possible for example to visualize what two bacteria have in common e g the genes of detoxification they both possess in which respect they differ ot whether they will be able to live together in some particular environment e g do they each perform part of a particular detoxification process thus enabling life where both bacteria alone could not have lived 14 OxyGene 3 5 1 Viewing Maps By clicking on a map name in the list of the maps appearing in the lower left corner of the
28. mit two different kinds of requests to OxyGene a What are the oxidative stress genes that are present in some given genomes b What are the genomes that contain an instance of a given OxyDB gene Depending on the question the bio analyst needs to check the appropriate radio button Search by Genome by Gene Question a Select Search by Genome Question b Select Search by Gene User Guide 5 3 2 1 Search by Genome The genomes within which the biologist wants to search for OxyDB genes must then be selected In this task the biologist can be aided by using the editable field Zr to enter parts of the genome names Available Genome s by Organism by Phylogeny brucella Online Genomes E T Brucella_abortus_9 941 Brucella_melitensis Brucella_melitensis_biovar_Abortus Brucella_ovis Brucella_suis_1330 or by using the combo box Sms Genomes where groups of pre selected genomes can be defined see later The button can be used to remove one such group The biologist may use the Shiftt Click interval selection or Ctrl Click combinations disjoint selection Click for Mac users to select several genomes at once The genomes may also be selected from their phylogenetic group by clicking on the corresponding by Phylogeny radio button Available Genome s by Organism by Phylogeny f 7 Bacteria 0 Y L7 Proteobacteria Y 1 Alphaproteobacteria v
29. n for all submitted genomes For example the detoxification subsystem of a particular bacteria shows all detoxification genes the bacteria possesses within its genome and how their corresponding enzymes are used to detoxify the oxidative compounds such as O or H O The Maps zab looks like this B OxyGene Version 1 0 5 E Knowledge Input Tables Sequences Maps Localisation Representation Comparison Remove Map Save as JPeg View _Number of Paralogs B map001 Detoxification Subsystem Reference map002 Acidobacteria bacterium Ellin345 Nb Paralogs Function Detoxification map Acidobacteria bacterium Ellin345 Es OxyGene B SIC UMR6026 2008 2 e ry i f Ao 1 3 Absence O Presence 1 a A j Or H02 Font Color mam Compound Symbol Name foRosm orn ike Mi Show Grayed Reference x gt u map001 Detoxification Subsystem Reference map002 Acidobacteria bacterium Ellin345 OHR_LKE al map003 Acidothermus cellulolyticus 118 R OOH R OH map004 Acidovorax avenae subsp citrulli AACOO map005 Acidovorax sp JS42 GSH_PRX PRXARP map006 Acinetobacter baumannii AYE aia ee gt m map007 Acinetobacter baumannii ATCC 17978 ONOOH NOx NO k INOR_BLG gt u N20 It includes a list of all available maps the reference map one map for every genome appearing at the lower left corner of the client w
30. owing all details of all homologs of the OxyDB genes found Associate a Function confidence level with each OxyDB gene class and an Annotation confidence level with each particular instance of such a gene with regard to objective criteria Identify already annotated genes re annotated genes because of a new start and genes found de novo furthermore isolate fragments frameshifts or pseudogenes for precise definitions see Thybert amp al 2008 e View the detoxification subsystem of any sequenced bacterial genome this subsystem is a subset of the reference detoxification subsystem which displays all known enzymatic potentialities of all sequenced bacteria Compare and view a combination of detoxification subsystems to see what different bacteria have in common what oxidative compounds some union of bacteria can detoxify etc e View and compare the localisation of the oxidative stress genes on the replicons of any sequenced bacterial genomes 2 OxyGene 2 Installation amp Launch of the Application OxyGene is a client server application with the server installed and staying at OUEST genopole Bio Informatics Platform keeping all needed pre computed genomic data while the OxyGene Client or GUI is a Java application which communicates with the server via web services The OxyGene Client needs to be downloaded on your computer and can be found on web site http www umr6026 univ rennesl fr english home research
31. per part of the window to achieve this a new client window will open automatically request all genomes containing that OxyDB gene from the server Search by Gene request process all these genomes and display the Number of Paralogs table on those genomes see Figure 5 It can be checked then that the column corresponding to that gene i e for all submitted genomes always contains at least one instance of that gene User Guide 3 3 2 The Genes Table 11 Another table which is available within OxyGene is the Genes table which recapitulates in a single table all information concerning the specific instances of the OxyDB genes found The table presents for each genome all its replicons and for each replicon all the OxyDB gene instances found together with their OxyDB name number annotation confidence level usual annotation name locus tag begin amp end positions frame NCBI and KEGG web references The Genes Tables is shown in Figure 9 The latter two properties are written in blue italic and are clickable this action will open your favourite web browser on the corresponding page NCBI or KEGG page of the considered gene Finally a Save Table button S enables the user to save the table under text txt or Microsoft Excel xls files N aey OxyGene Version 1 0 5 r r Knowledge Input Tables Sequences Maps Localisation Genomes Table Genes Table Phylum Level 0 F Save T
32. re 6 The different shades of the same colour represent different numbers of paralogs The legend on the right hand side of the table indicates the colours used to represent each number B OxyGene Version 1 0 5 ti Knowledge Input Tables Sequences Maps Localisation Genomes Table Genes Table View Number of Paralogs Annotation Score Phylum Level 2 Save Table Genome Phylum CAT_MON CAT_GAT CAT_SRP CAT_BFL CAT_MNG SOD_FMN SOD_CUZ SOD_NKL OHR_OHR OHR_OSM OHR_LKE HPX_HPX a Acidobacteria bacterium Ellin345 Acidobacteriales 0 0 0 1 1 1 0 0 0 1 1 Acidothermus cellulolyticus 118 Actinobacteridae 1 0 0 0 0 0 o F o 1 0 0 aa Acidovorax avenae subsp citrulli AACOO Betaproteobacteria 1 1 0 i 0 2 2 0 1 1 1 0 E Acidovorax sp JS42 Betaproteobacteria 1 1 0 0 0 1 1 0 1 1 1 0 Acinetobacter baumannii AYE Gammaproteobacteria 0 1 1 E o 1 1 0 1 i 1 0 0 Acinetobacter baumannii ATCC 17978 Gammaproteobacteria 1 1 1 1 o 1 1 0 g 0 1 1 Figure 6 The Number of Paralogs table shows the number of paralogs for all OxyDB genes for all submitted genomes with different shades of the same colour to represent different numbers i 3 a j n The tadio buttons Vit C Number of Paralogs Annotation Score a allows the biologist to switch to the Annotation Confidence Levels table and back The latter confidence levels shown in Figure 7 presents all different paralogs identified by their locus tag for all OxyDB g
33. s altogether then press the Add button to view the sequences For each instance of the selected OxyDB gene class in the selected genome a line will be added to the table showing the genome name OxyDB gene name amp number its usual annotation gene name locus tag and the actual sequence of the gene instance gt gt If AW submitted Genomes and All Genes found are respectively selected in the Genome and Gene combo boxes then all instances of all OxyDB genes of all submitted genomes will be added to the table If AW submitted Genomes is selected and a single particular OxyDB gene class is selected then all instances of that gene in all submitted genomes i e all paralogs and orthologs will be added to the table This option enables the biologist to compare the different sequences implementing a particular OxyDB gene If a single particular genome is selected and AX Genes found is selected then all instances of all OxyDB genes of that genome will be added to the table If a single particular genome is selected and a single particular OxyDB gene class is selected then all instances of that gene in that genome i e all paralogs will be added to the table To remove lines from the table the user simply needs to select the desired lines within the table in the usual manner and then press the remove button The sequences may be written in nucleic or proteic form To switch form simply select the appropriate radio button
34. tton The frame thickness around the enzyme boxes represents the function confidence level which is associated to each OxyDB gene class The biologist may want to view the number of paralogs rather than the annotation confidence level This can be achieved by selecting Number of Paralogs within the View combo box at the top of the panel The map is then replaced by Figure 10 and the legend by View Number of Paralogs HA Nb Paralogs Function m E m fF 1 Absence O Presence 1 Font Color Compound Symbol Name v Show Grayed Reference The last colour the Presence represented in grey cannot be changed and is used in the domain reference maps and in combination maps see below It is possible to remove a particular map by selecting it from the list in the lower left corner and pressing the Remove Map button Remove Map T ikewise to save a particular map under jpeg form first select it from the same list then adjust the colours symbols and greyed items as desired and eventually press the Save as JPeg Save as Peg button the definition of the file name 1a dialog window will appear enabling the selection of the repertory and At last clicking on non empty gene boxes triggers the opening of the corresponding gene window as seen in Figure 10 The maps in OxyGene were generated using the free Java library JGraphyar that allows the production of graph visualization and layouts within Java pro
35. umber of maps results in a map showing the presence of genes present in a original maps e Union of any number of maps results in a map showing the presence of genes present in at least one of the original maps Difference between exactly vo maps results in a map showing the presence of genes that are present in one of the two maps but wot in the other These operations are achieved by selecting the Comparison tab in the upper left panel of the client window An appropriate interface appears Representation Comparison Union Intersection Difference map040 Acidobacteria bacterium Ellin34 map041 Acidothermus cellulolyticus 11B map042 Acidovorax avenae subsp citrulli map043 Acidovorax sp JS4 2 map044 Delftia acidovorans SPH 1 Name 30 chars max add map001 Detoxification Subsystem nse User Guide 17 It enables the user to easily select in the usual manner a number of different maps within the list provided which contains all maps including previous constructed combinations to choose the desired operation by selecting the adequate radio button and finally to give a new name to the newly defined map Then just press the Add button the new map will appear on the right hand side frame and its name will be added to the lists of map names on the left hand side of the client window A mathematical name is supplied by default For instance constructing the difference between Acidi
36. vorax avenae subsp citrul and Acidovorax sp JS42 subsystems is achieved thus Representation Comparison O Union Intersection Difference map002 Acidobacteria bacterium Ellin345 map003 Acidothermus cellulolyticus 11B map004 Acidovorax avenae subsp citrulli map005 Acidovorax sp JS42 map006 Delftia acidovorans SPH 1 n lt gt Add map001 Detoxification Subsystem ennaa Name 30 chars max 3 map004 map005 and produces the following map map001 Detoxification Subsystem Reference map011 a map004 map005 Detoxification map d map004 map005 OxyGene B SIC UMR6026 2008 A 0z a H202 A H20 X no oO gt u N20 The presence of genes in the resulting combination maps is represented by a greyed background box around the gene name whereas the absence if displayed at all recall Show greyed Reference check box is denoted by a white or just no background as usual Clicking on the gene boxes here does not trigger the appearance of the gene window since it is unclear what genes should be associated to these logical operations 18 OxyGene 3 6 The Localisation tab The localisation tab is the last of the bio analysis tabs provided It enables the biologist to view the distribution of the OxyDB instances on the genome replicons It makes use of the CGView Java library developed by Stothard P and Wishart DS supplie
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