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Anotation Process

Scenario 3. Anotation Process .

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Anotation Process

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  1. Scenario 3 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 Show3. Click Continue button Continue

  2. Scenario 3 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

  3. Main Menu Options Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis 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. Main Menu Options Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none N6,N4 DNA methyltransferase (PF01515): 2e-18 Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis 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..

  5. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none PvuIIM: DNA methyltransferase (NP_072082): 8e-64 Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis 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. 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 Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)PredictedLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase Predicted Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis You begin to suspect the annotated start codon. To visualize alternatives, click on the Options button, then click on Show alternate starts. Options

  7. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none 1533628 and upstream:CTTCCGGGAAATCCTGTG 1533931 and upstream:TAACTTAAATGTCGCTTG Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis 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

  8. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis 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. 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 Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis 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. Neisseria meningitidis More Options

  10. Main Menu Annotate Options Options History Anabaena PCC 7120: all1290 GraphicGenome Alignment with homologs Alignment with motif 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 View Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none Alignment with motif Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis Click on Alignment with motifto see how All1120 compares to other protein that make up the Pfam motif represented by the motif bar. Neisseria meningitidis More

  11. PubMed Nucleotide Protein Structure CDD Taxonomy Help Conserved Domain Database CD: Pfam01555.5, N6_N4_Mtase PSSM-Id: 8054 Source: 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: Created: Alignment from source 13-Jun-2002 Aligned: 52 rows PSSM: 199 columns Representative: Consensus [Click here for CDART summary of Proteins containing pfam01555] Proteins: with  Cn3D using  Virtual Bonds (To display structure, download Cn3D) View 3D Structure Subset Rows up to 10 of the most diverse members 10 20 30 40 50 60 ....*....|....*....|....*....|....*....|....*....|....*....| All129078KRVLTENGSFILDLGgaylpgnp----VRSIYQYELLVKLCKEVGFFL----------- 122 consensus 1 ARRVLKPDGSIFIFGG------------NKSQKNIFRFIDILIEKGFKF-----------37 Pvuii Dna Methyltransfer77 DGSFVVDFGGAYMKGVp-----------ARSIYNFRVLIRMIDEVGFFL-----------114 Modification methylase S119 PRTGWKRNKQLSLVP--------------------FRVALALQDDGWWI-----------147 BglI modification methyl92 FQAVNLKKHRVSVTREd----------iLNALKLEPELTKYQLAKKFNCs---------e132 adenine specific DNA met174 ARDLLKEDGVIFISIDdnecan-lkilcDEIFGEDNFVGDFIRKTKSTTndakiglnyqh232 adenine specific DNA met131 ILRTLLPIYARALKDLmrt------iknVFKQKGQAQAQLVLKEQIKELs---------q175 Modification methylase M133 IIDPFMGSGTTLVQCMem--------giNSIGIDISPFNCLIAEVKLQKydi------qk178 Modification methylase M178 LSRCNLKDGDYILDPFagtgttgavvkkMKYQLYPKDLNVILIEKGKKF-----------226 Modification methylase B134 SHIAFEPKSFIFEYNLeeldraykeiyeISPTKIEQKFNHLSITEGAFPeete----ndl189 gi_3257411123 ANTYAMPSELILKGFP-------------KVKDVVLLFVDDKVLVGETVr----------159 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 toget to the best part of the alignment. More More Back to Annotation

  12. PubMed Nucleotide Protein Structure CDD Taxonomy Help Conserved Domain Database 310 320 330 340 350 360 ....*....|....*....|....*....|....*....|....*....|....*....| All1290 228rrcKAAGVKPHPARFPQGFAEFFIKFLTD-------------------EGDLVLDPFAGS 268 consensus 131 ---NLKGKKKHPTQKPEALLERIILESSN-------------------EGDLVLDPFAGS168 Pvuii Dna Methyltransfer223 ancKLMGIKAHPARFPAKLPEFFIRMLTE-------------------PDDLVVDIFGGS263 Modification methylase S339 sipTAPSGANHFAVMPRKLAHFALKATLP-------------------MNGSCLDPFMGS379 BglI modification methyl238 ---SVRKNDDHEAKFPLLLPQRLIKLLTQ-------------------KGDTVLDCFMGS275 adenine specific DNA met367 ellNLGMGEYFTYPKGVEFMKKIILHSTTp-----------------nEGDIILDFFAGS409 adenine specific DNA met279 ----LGLKGLFKTPKPVALIKYLLLCSTP-------------------KDSIILDFFAGS315 Modification methylase M329 vfdPYYCYKHKKICRPVQTILRHLEEYTNdvisri-------eefskiRKDAYYLIINGD381 Modification methylase M464 icyNCQKEIYGKNSLPILKESKEIIESLEsvengeyqvgenikpqyqkRCKESKSKFAGM523 Modification methylase B319 tspPYCNRYDYTRTYALELAYLGVDEKKIrelrqa-------qlsctvENKSKLKQLKDY371 gi_3257411255 ---KVCDVRRLRKCFPRTRFDAIITEPYM-------------------GKPLKYKPSRGE292 370 380 390 400 410 ....*....|....*....|....*....|....*....|....*....|....*. All1290 269NTTGFVAETW-----------QRRWIAVEINQDYVLGS--------------RYRF299 consensus 169 GTTAAAAKEL-----------GRKFIGIEINEEYVKLA--------------KKRL199 Pvuii Dna Methyltransfer264 NTTGLVAERE-----------SRKWISFEMKPEYVAAS--------------AFRF294 Modification methylase S380 GTTGRVVREL-----------GGRFVGVDVNEHYMTDY--------------LVES410 BglI modification methyl276 GTTAVAALSE-----------SRNFIGIEKEPKYIQLS--------------NKNV306 adenine specific DNA met410 GTTVHAVMELnae-----dkgNREFILVQIDEEIKEDEsay--------dfcKKEL452 adenine specific DNA met316 GTTAQAVIEV-----------NRDYCLNWSFYLCQKEE--------------KIKN346 Modification methylase M382 SRTVDIEEELkkhpnfyelykNKKIDGIFTSPPYLGQIdyheqhayayelfdIPRL437 Modification methylase M524 ERMNWGASPG-----------ARKTIIGDSFSKMRLYR--------------LDQP554 Modification methylase B372 YHSLFLESRYae--------iERLVTGNEVLNEINYAL--------------RKRW405 gi_3257411293 AIKIAKGLDR------------LYYQAFESFADVLKRGs-------------IIVF323 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 Annotation More Back to Annotation

  13. Options GraphicGenome Alignment with homologs Alignment with motif 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 Alignment with homologs Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-GTG)SystemLength = 200 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis 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. Neisseria meningitidis More Options

  14. Main Menu Annotate Options History Anabaena PCC 7120: all1290 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 Continue

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

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

  18. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-TTG) PredictedLength = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferase Predicted Cyanobacterial orthologs: none 1533931 Justification IC: Inferred by curatorIDA: 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 IC: Inferred by curatorUse this when your assertion is based on your own judgement of sequence similarity or other information, when there is no direct experimental data. IC: Inferred by curator Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis 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. Neisseria meningitidis More

  19. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533628 (start-TTG) PredictedLength = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferase Predicted Cyanobacterial orthologs: none 1533931 Justification IC: Inferred by curatorIDA: 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 IC: Inferred by curator Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis Inferred by curator seems to fit the situation. Click on it. Neisseria meningitidis More

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

  21. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533931 (start-TTG)HumanLength = 301 amino acids Strand: Complementary Function: PvuII DNA methyltransferase System Cyanobacterial orthologs: none A Anab7120 Proteus vulgaris Salmonella paratyphi Streptomyces spectabilis Streptomyces netropsis 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 . Neisseria meningitidis Continue More Continue

  22. Main Menu Annotate Options History Anabaena PCC 7120: all1290 Replicon: Chromosome Coordinates: 1533026 (stop) <- 1533931 (start-TTG)HumanLength = 301 amino acids Strand: Complementary Gene name(s): avaXM Function: Putative type II DNA cytosine methyltransferase (CAGCTG-specific) HumanClassification: Type II beta (N4) Human Activity: Protects against: PvuII ExperimentIn vivo activity: existsExperiment Cyanobacterial orthologs: none A A A A A Anab7120 Proteus vulgaris Salmonella paratyphi That’s how the annotation ends up. Now anyone clicking on HumanorExperiment 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. Streptomyces spectabilis A End More

  23. Scenario 3 Anotation ProcessSummary • 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 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.

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