1. Anotation Process What follows is a simulation of the process of annotating, using the proposed graphical interface. The interface does not yet exist. As you go through the simulation please consider what capabilities you would want to serve your research and annotation interests. A narrative to help you go through the simulation appears in a red-bordered box, such as the one below. To begin: 1. Click on Slide Show, (on the upper toolbar) 2. Click View Show 3. Click Continue button Continue Scenario 3

2. Anotation Process You find yourself annotating a set of genes that includes all1290 from Anabaena PCC 7120. You want to assess the validity of the automated annotation, particularly the assertion of function and start codon. If there are any problems, you want to fix them. Continue Scenario 3

3. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Options Annotate Main Menu History Evidently no human has touched this annotation (System is given as the only source). Is the functional annotation sound? Mouse over* to the blue motif bar above the graphical representation of all1290. *In real life, information will pop up when you mouse to an informative position. In this simulation you’ll also need to click.

4. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Options Annotate Main Menu History Pfam found a motif consistent with the annotation with a good expectation value. Curiously, the motif extends beyond the start of the gene. Mouse away from the bar.* *In real life, information will go away when you mouse away from an informative position. In this simulation you’ll also need to click anywhere.. N6,N4 DNA methyltransferase (PF01515): 2e-18

5. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History PvuIIM: DNA methyltransferase (NP_072082): 8e-64 Mouse over to the first aligned gene, from Proteus vulgaris. Again, good support, and again, the gene extends beyond the annotated start codon of the Anabaena orf. *Remember to click to view the popup and click to make it disappear.

6. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)Predicted Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferasePredicted Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotateMain MenuHistory You begin to suspect the annotated start codon. To visualize alternatives, click on the Options button, then click on Show alternate starts. Options View: graphic Show all Show hits: <1e-6 Show neighbors: +/- 1 Show motifs Show alternate starts Show annotated features Show predicted features Show transposon ends Show tandem repeats Show inverted repeats Show dispersed repeats Show private set Show alternate starts Options

7. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Mouse over to the annotated start site* and you see the sequence preceding it: a plausible ribosome binding site. Mouse over to the most distant start site. Not as good. *Click to show, click to disappear 1533628 and upstream: CTTCCGGGAAATCCTGTG 1533931 and upstream: TAACTTAAATGTCGCTTG

8. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Nonetheless, the position of the distant site relative to the other sequences makes it a reasonable candidate. Click on it to provisionally change the start site.

9. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More Much better! More similarity and more sequences that are similar (and better E-values, too, if you were to look). However, it is always a good practice to check the alignment before accepting the conclusions of a similarity search, so click on button. and then on View. Options View: graphic Show all Show hits: <1e-6 Show neighbors: +/- 1 Show motifs Show alternate starts Show annotated features Show predicted features Show transposon ends Show tandem repeats Show inverted repeats Show dispersed repeats Show private set View Options

10. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More Click on Alignment with motif to see how All1120 compares to other protein that make up the Pfam motif represented by the motif bar. View Show all Show hits: <1e-6 Show neighbors: +/- 1 Show motifs Show alternate starts Show annotated features Show predicted features Show transposon ends Show tandem repeats Show inverted repeats Show dispersed repeats Show private set Options Graphic Genome Alignment with homologs Alignment with motif View Alignment with motif

11. Back to Annotation 10 20 30 40 50 60....*....|....*....|....*....|....*....|....*....|....*....| All1290 78 KRVLTENGSFILDLGgaylpgnp----VRSIYQYELLVKLCKEVGFFL----------- 122 consensus 1 ARRVLKPDGSIFIFGG------------NKSQKNIFRFIDILIEKGFKF----------- 37 Pvuii Dna Methyltransfer 77 DGSFVVDFGGAYMKGVp-----------ARSIYNFRVLIRMIDEVGFFL----------- 114 Modification methylase S 119 PRTGWKRNKQLSLVP--------------------FRVALALQDDGWWI----------- 147 BglI modification methyl 92 FQAVNLKKHRVSVTREd----------iLNALKLEPELTKYQLAKKFNCs---------e 132 adenine specific DNA met 174 ARDLLKEDGVIFISIDdnecan-lkilcDEIFGEDNFVGDFIRKTKSTTndakiglnyqh 232 adenine specific DNA met 131 ILRTLLPIYARALKDLmrt------iknVFKQKGQAQAQLVLKEQIKELs---------q 175 Modification methylase M 133 IIDPFMGSGTTLVQCMem--------giNSIGIDISPFNCLIAEVKLQKydi------qk 178 Modification methylase M 178 LSRCNLKDGDYILDPFagtgttgavvkkMKYQLYPKDLNVILIEKGKKF----------- 226 Modification methylase B 134 SHIAFEPKSFIFEYNLeeldraykeiyeISPTKIEQKFNHLSITEGAFPeete----ndl 189 gi_3257411 123 ANTYAMPSELILKGFP-------------KVKDVVLLFVDDKVLVGETVr---------- 159 Conserved Domain Database PubMedNucleotideProteinStructureCDDTaxonomyHelp CD:Pfam01555.5, N6_N4_MtasePSSM-Id:8054Source: Pfam[US], Pfam[UK] Description: DNA methylase. Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. Taxa: root Status: Alignment from source Created: 13-Jun-2002 Aligned:52 rowsPSSM:199 columnsRepresentative:Consensus Proteins: [Click here for CDART summary of Proteins containing pfam01555] View 3D Structure Subset Rows with Cn3D using Virtual Bonds (To display structure, download Cn3D) up to 10of the most diverse members More This is output from NCBI showing the alignment that went into making Pfam motif 01555... but it was intercepted by the interface in order to incorporate the sequence of All1290 for comparison. Click on to get to the best part of the alignment. More

12. Conserved Domain Database PubMedNucleotideProteinStructureCDDTaxonomyHelp 310 320 330 340 350 360....*....|....*....|....*....|....*....|....*....|....*....| All1290 228 rrcKAAGVKPHPARFPQGFAEFFIKFLTD-------------------EGDLVLDPFAGS 268 consensus 131 ---NLKGKKKHPTQKPEALLERIILESSN-------------------EGDLVLDPFAGS 168 Pvuii Dna Methyltransfer 223 ancKLMGIKAHPARFPAKLPEFFIRMLTE-------------------PDDLVVDIFGGS 263 Modification methylase S 339 sipTAPSGANHFAVMPRKLAHFALKATLP-------------------MNGSCLDPFMGS 379 BglI modification methyl 238 ---SVRKNDDHEAKFPLLLPQRLIKLLTQ-------------------KGDTVLDCFMGS 275 adenine specific DNA met 367 ellNLGMGEYFTYPKGVEFMKKIILHSTTp-----------------nEGDIILDFFAGS 409 adenine specific DNA met 279 ----LGLKGLFKTPKPVALIKYLLLCSTP-------------------KDSIILDFFAGS 315 Modification methylase M 329 vfdPYYCYKHKKICRPVQTILRHLEEYTNdvisri-------eefskiRKDAYYLIINGD 381 Modification methylase M 464 icyNCQKEIYGKNSLPILKESKEIIESLEsvengeyqvgenikpqyqkRCKESKSKFAGM 523 Modification methylase B 319 tspPYCNRYDYTRTYALELAYLGVDEKKIrelrqa-------qlsctvENKSKLKQLKDY 371 gi_3257411 255 ---KVCDVRRLRKCFPRTRFDAIITEPYM-------------------GKPLKYKPSRGE 292 370 380 390 400 410....*....|....*....|....*....|....*....|....*....|....*. All1290 269 NTTGFVAETW-----------QRRWIAVEINQDYVLGS--------------RYRF 299 consensus 169 GTTAAAAKEL-----------GRKFIGIEINEEYVKLA--------------KKRL 199 Pvuii Dna Methyltransfer 264 NTTGLVAERE-----------SRKWISFEMKPEYVAAS--------------AFRF 294 Modification methylase S 380 GTTGRVVREL-----------GGRFVGVDVNEHYMTDY--------------LVES 410 BglI modification methyl 276 GTTAVAALSE-----------SRNFIGIEKEPKYIQLS--------------NKNV 306 adenine specific DNA met 410 GTTVHAVMELnae-----dkgNREFILVQIDEEIKEDEsay--------dfcKKEL 452 adenine specific DNA met 316 GTTAQAVIEV-----------NRDYCLNWSFYLCQKEE--------------KIKN 346 Modification methylase M 382 SRTVDIEEELkkhpnfyelykNKKIDGIFTSPPYLGQIdyheqhayayelfdIPRL 437 Modification methylase M 524 ERMNWGASPG-----------ARKTIIGDSFSKMRLYR--------------LDQP 554 Modification methylase B 372 YHSLFLESRYae--------iERLVTGNEVLNEINYAL--------------RKRW 405 gi_3257411 293 AIKIAKGLDR------------LYYQAFESFADVLKRGs-------------IIVF 323 Note that All1290 matches the alignment in almost all of the most informative positions (in red), those presumably related to common function. Click on Back to AnnotationMore Back to Annotation

13. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More Since the motif does not extend to the beginning of the protein, it might be a good idea to check alignment with the full length of protein identified by the similarity search. Click on button then on View, and finally on Alignment with homologs. Options View: graphic Show all Show hits: <1e-6 Show neighbors: +/- 1 Show motifs Show alternate starts Show annotated features Show predicted features Show transposon ends Show tandem repeats Show inverted repeats Show dispersed repeats Show private set View Options Graphic Genome Alignment with homologs Alignment with motif Alignment with homologs

14. Anabaena PCC 7120: all1290 OptionsAnnotate Main Menu History NmeSIM (Neisseria) 3 ---TISSIMSLEN---------------FQLIKTQLGVPSYEND--RVAIYQGDCIQLMD ScaIM (Streptomyces) 6 FGYVIQSSAALWNRLSTFSQRGKALDTRLADIKKALGKPYYETS--DVLLYHGDSLELLK All1290 (Anabaena) 1 LNSQQTTTIKLTN-----------------------FIPSYTQQ--HGAVYLGDCLEIIK PvuIIM (Proteus) 6 LQTMSSNDMLNFG-----------------------KKPAYTTS--NGSMYIGDSLELLE SptAIM (Salmonella) 1 --------MMFDD-----------------------KKPAYKTD--LGAMYIADSLEMLE SpcM (Streptomyces) 1 ----MTESTTAAG-----------------------DRRALGAE--HGSYHWGDSLALLE SpcG (Streptomyces) 1 ----MTELT-PTE-----------------------DRCPLEAE--HGSYHWGNSLELMK BglIIM (Bacillus) 5 QYKQIKLHLGMED---D-----------NEDLPNHIPSSFPKQH--LNKIYNGDTMNMLL MJ1498 (Methanococcus) 1 ------------------------------------------ME--INKIYCMDCLEGMK CfrBIM (Citrobacter) 66 VINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKKIISKSPLNNMLLQGNCAETLK BamHIM (Bacillus) 68 KILENKNSVKLNEFN-----------------SIQEIKPYFYTD--LGKLYNGDCLELFK NmeSIM (Neisseria) 43 KISKGSFQMTITSPPYNIGKEYES----ILDLEHYLEWCERWMQSIHHLTEDSGCFWLNL ScaIM (Streptomyces) 64 SMPQQIFDLTVTSPPYNIGKEYEG----VLSIEEYISWCETWMSRVHRATSAGGAFWLNV All1290 (Anabaena) 36 SIPDNSVNLILTSPPFALTRKKEYG---NESAEKYIEWFLPFADEFKRVLTENGSFILDL PvuIIM (Proteus) 41 SFPDESISLVMTSPPFALQRKKEYG---NLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDF SptAIM (Salmonella) 28 SMPDNSLNLVMTSPPFALQRKKEYG---NHDQEQYIDWFLKFGELVFKKLKDDGSFVVDF SpcM (Streptomyces) 32 GVPDGSVRAVVCSPPFEGPQLIADE---DRAGACSSDWLMPFFGQFERVLRPDGCVAFEL SpcG (Streptomyces) 32 GIPDASVDAVVCSPPFEGDALISDE---GRRGDAFVAWIEPFFRQFQRVLRPAGCVAFEL BglIIM (Bacillus) 49 DIPDNSVDLVVTSPPYNINKFKND----RRPLEEYLKWQTEIIEQCHRVLKPSGSIFWQV MJ1498 (Methanococcus) 17 QLKDKTVDVVVTSPPYNIGIKYNKYSD-NLSREDYLNWIEEVVKEIKRVLKDDGSFFINV CfrBIM (Citrobacter) 126 KLPDESVNLVFTSPPYYNAKPEYS--E-YHTYDEYLSLLRSVIKECHRVLSEGRFFVINV BamHIM (Bacillus) 68 QVPDENVDTIFADPPFNLDKEYDEGVTDKNSFSGYLDWYYKWIDECIRVLKPGGSLFIYN To one knowledgeable on DNA methyltransferases, the identity of All1290 at positions 48-51 (SPPF) is particularly striking, as that is part of the AdoMet binding site and one of the signatures of N4-cytosine methyltransferases. Press. Continue

15. Anabaena PCC 7120: all1290 OptionsAnnotate Main Menu History NmeSIM (Neisseria) 3 ---TISSIMSLEN---------------FQLIKTQLGVPSYEND--RVAIYQGDCIQLMD ScaIM (Streptomyces) 6 FGYVIQSSAALWNRLSTFSQRGKALDTRLADIKKALGKPYYETS--DVLLYHGDSLELLK All1290 (Anabaena) 1 LNSQQTTTIKLTN-----------------------FIPSYTQQ--HGAVYLGDCLEIIK PvuIIM (Proteus) 6 LQTMSSNDMLNFG-----------------------KKPAYTTS--NGSMYIGDSLELLE SptAIM (Salmonella) 1 --------MMFDD-----------------------KKPAYKTD--LGAMYIADSLEMLE SpcM (Streptomyces) 1 ----MTESTTAAG-----------------------DRRALGAE--HGSYHWGDSLALLE SpcG (Streptomyces) 1 ----MTELT-PTE-----------------------DRCPLEAE--HGSYHWGNSLELMK BglIIM (Bacillus) 5 QYKQIKLHLGMED---D-----------NEDLPNHIPSSFPKQH--LNKIYNGDTMNMLL MJ1498 (Methanococcus) 1 ------------------------------------------ME--INKIYCMDCLEGMK CfrBIM (Citrobacter) 66 VINSKTSTIDYKKSSKSPFLIKKAMEVVHTPKKVKKEKKIISKSPLNNMLLQGNCAETLK BamHIM (Bacillus) 68 KILENKNSVKLNEFN-----------------SIQEIKPYFYTD--LGKLYNGDCLELFK NmeSIM (Neisseria) 43 KISKGSFQMTITSPPYNIGKEYES----ILDLEHYLEWCERWMQSIHHLTEDSGCFWLNL ScaIM (Streptomyces) 64 SMPQQIFDLTVTSPPYNIGKEYEG----VLSIEEYISWCETWMSRVHRATSAGGAFWLNV All1290 (Anabaena) 36 SIPDNSVNLILTSPPFALTRKKEYG---NESAEKYIEWFLPFADEFKRVLTENGSFILDL PvuIIM (Proteus) 41 SFPDESISLVMTSPPFALQRKKEYG---NLEQHEYVDWFLSFAKVVNKKLKPDGSFVVDF SptAIM (Salmonella) 28 SMPDNSLNLVMTSPPFALQRKKEYG---NHDQEQYIDWFLKFGELVFKKLKDDGSFVVDF SpcM (Streptomyces) 32 GVPDGSVRAVVCSPPFEGPQLIADE---DRAGACSSDWLMPFFGQFERVLRPDGCVAFEL SpcG (Streptomyces) 32 GIPDASVDAVVCSPPFEGDALISDE---GRRGDAFVAWIEPFFRQFQRVLRPAGCVAFEL BglIIM (Bacillus) 49 DIPDNSVDLVVTSPPYNINKFKND----RRPLEEYLKWQTEIIEQCHRVLKPSGSIFWQV MJ1498 (Methanococcus) 17 QLKDKTVDVVVTSPPYNIGIKYNKYSD-NLSREDYLNWIEEVVKEIKRVLKDDGSFFINV CfrBIM (Citrobacter) 126 KLPDESVNLVFTSPPYYNAKPEYS--E-YHTYDEYLSLLRSVIKECHRVLSEGRFFVINV BamHIM (Bacillus) 68 QVPDENVDTIFADPPFNLDKEYDEGVTDKNSFSGYLDWYYKWIDECIRVLKPGGSLFIYN The substantial agreement between All1290, PvuIIM, and SptAIM turns out to extend through the DNA recognition domain. That’s good enough for me! Let’s start making this public by clicking. Annotate

16. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More That click gets you back to the annotation page. Let’s begin by changing the start site. Click Start site.. Coordinates Start site Gene name Function Comment Internal note Remove orf Start site Annotate

17. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)System Length = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More You could type in the new coordinate, but it’s easier just to click on the new start site. 1533628

18. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-TTG)Predicted Length = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferasePredicted Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More Every assertion must be accompanied by a justification. The codes are standard from the Gene Ontology Consortium and facilitate searching. Mouse over to IC to find out what it’s used for. 1533931 IC: Inferred by curator IC: Inferred by curator Use this when your assertion is based on your own judgement of sequence similarity or other information, when there is no direct experimental data. Justification IC: Inferred by curator IDA: Inferred by direct assay IEP: Inferred from expression pattern IGI: Inferred from genetic interaction IMP: Inferred from mutant phenotype IPI: Inferred from physical interaction TAS: Traceable author statement NAS: Nontraceable author statement ND: No biological data available

19. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-TTG)Predicted Length = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferasePredicted Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More Inferred by curator seems to fit the situation. Click on it. 1533931 IC: Inferred by curator Justification IC: Inferred by curator IDA: Inferred by direct assay IEP: Inferred from expression pattern IGI: Inferred from genetic interaction IMP: Inferred from mutant phenotype IPI: Inferred from physical interaction TAS: Traceable author statement NAS: Nontraceable author statement ND: No biological data available

20. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-TTG)Human Length = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferasePredicted Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More You would now fill in the reasons leading you to your assertion regarding the start codon. For now, just press the Enter key. 1533931 Comment

21. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533931 (start-TTG)Human Length = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferaseSystem Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History Streptomyces netropsis Neisseria meningitidis More The start codon has been changed. In a like fashion, a name is given to the orf, and functional annotation added. Now that the activity seems real, I’m inspired to look through the literature, and... it turns out that Bancroft et al (1989) described in vivo protection of Anabaena DNA against PvuII! Press. A Continue

22. Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533931 (start-TTG)Human Length = 301 amino acids Strand: Complementary Gene name(s): avaXM Function: Putative type II DNA cytosine methyltransferase (CAGCTG-specific)Human Classification: Type II beta (N4)Human Activity: Protects against: PvuII Experiment In vivo activity: existsExperiment Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis OptionsAnnotate Main Menu History More End A A A A A That’s how the annotation ends up. Now anyone clicking on Human or Experiment will find the annotations you made, and anyone mousing over one of the annotator icons ( ) will get to your name, and your e-mail address. A

23. Anotation Process Summary Each assertion is accompanied by a justification linked to the annotator Interface provides tools for trying out different start codons and assessing their validity Interface provides different alignments for the assessment of orf function In the end, human expertise is required to recognize the critical information Scenario 3 There are no new tools here, just a comprehensive interface to put these tools at the service of human annotators who prefer to do science rather than click keys. The proposal seeks resources to support the development of this interface. To quit, right click, then click End Show.