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Volumn , Issue , 2009, Pages 315-335

Microbial Genomics of Aquaculture Pathogens

Author keywords

Comparative genomics and global comparisons to sequenced genomes; ERGO graphical interface of msa1 gene from R. salmoninarum genome; Genome assembly and gap closure; Infectious disease and economic loss in aquaculture; Microbial genomics of aquaculture pathogens; Molecular advances in genomics and pathogen biology understanding; Post Sanger strategies for de novo sequencing; Sequencing errors and assembly errors in genome sequence data; Transitive annotation error; Whole genome shotgun method

Indexed keywords


EID: 84889400564     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780813807379.ch12     Document Type: Chapter
Times cited : (3)

References (64)
  • 3
    • 0142119484 scopus 로고    scopus 로고
    • Viewing and annotating sequence data with Artemis
    • Berriman, M., Rutherford, K. 2003. Viewing and annotating sequence data with Artemis. Briefings in Bioinformatics. 4:124-132.
    • (2003) Briefings in Bioinformatics , vol.4 , pp. 124-132
    • Berriman, M.1    Rutherford, K.2
  • 5
    • 0036888996 scopus 로고    scopus 로고
    • On the high value of low standards
    • Branscomb, E., Predki, P. 2002. On the high value of low standards. Journal of Bacteriology. 184:6406-6409.
    • (2002) Journal of Bacteriology , vol.184 , pp. 6406-6409
    • Branscomb, E.1    Predki, P.2
  • 7
    • 77951983076 scopus 로고    scopus 로고
    • The Economic Effects of Rainbow Trout Stocking by Fish andWildlife Service Hatcheries in FY 2004
    • U.S. Fish and Wildlife Service DoE, Arlington, VA
    • Caudill, J. 2005. The Economic Effects of Rainbow Trout Stocking by Fish andWildlife Service Hatcheries in FY 2004. U.S. Fish and Wildlife Service DoE, Arlington, VA.
    • (2005)
    • Caudill, J.1
  • 10
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using Phred. II. Error probabilities
    • Ewing, B., Green, P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research. 8:186-194.
    • (1998) Genome Research , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 11
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using Phred. I. Accuracy assessment
    • Ewing, B., Hillier, L.,Wendl, M.C., Green, P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Research. 8:175-185.
    • (1998) Genome Research , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 14
    • 34547912489 scopus 로고    scopus 로고
    • DoriC: A database of oriC regions in bacterial genomes
    • Gao, F., Zhang, C.T. 2007. DoriC: A database of oriC regions in bacterial genomes. Bioinformatics. 23:1866-1867.
    • (2007) Bioinformatics , vol.23 , pp. 1866-1867
    • Gao, F.1    Zhang, C.T.2
  • 15
    • 41349112730 scopus 로고    scopus 로고
    • Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes
    • Gao, F., Zhang, C.T. 2008. Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics. 9:79.
    • (2008) BMC Bioinformatics , vol.9 , pp. 79
    • Gao, F.1    Zhang, C.T.2
  • 16
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., Abajian, C., Green, P. 1998. Consed: A graphical tool for sequence finishing. Genome Research. 8:195-202.
    • (1998) Genome Research , vol.8 , pp. 195-202
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 17
  • 18
    • 28044463174 scopus 로고    scopus 로고
    • Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705
    • Guy, L., Karamata, D.,Moreillon, P.,Roten, C.A. 2005. Genometrics as an essential tool for the assembly of whole genome sequences: The example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiology. 5:60.
    • (2005) BMC Microbiology , vol.5 , pp. 60
    • Guy, L.1    Karamata, D.2    Moreillon, P.3    Roten, C.A.4
  • 19
    • 5444276316 scopus 로고    scopus 로고
    • Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication
    • Guy, L., Roten, C.A. 2004. Genometric analyses of the organization of circular chromosomes: A universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication. Gene. 340:45-52.
    • (2004) Gene , vol.340 , pp. 45-52
    • Guy, L.1    Roten, C.A.2
  • 20
    • 33947546580 scopus 로고    scopus 로고
    • Gene flow, effective population size and selection at major histocompatibility complex genes: Brown trout in the Hardanger Fjord, Norway
    • Hansen, M.M., Skaala, O., Jensen, L.F., Bekkevold, D., Mensberg, K.L. 2007. Gene flow, effective population size and selection at major histocompatibility complex genes: Brown trout in the Hardanger Fjord, Norway. Molecular Ecology. 16:1413-1425.
    • (2007) Molecular Ecology , vol.16 , pp. 1413-1425
    • Hansen, M.M.1    Skaala, O.2    Jensen, L.F.3    Bekkevold, D.4    Mensberg, K.L.5
  • 22
    • 36148979374 scopus 로고    scopus 로고
    • An evaluation of comparative genome sequencing (CGS) by comparing two previously-sequenced bacterial genomes
    • Herring, C.D., Palsson, B.O. 2007. An evaluation of comparative genome sequencing (CGS) by comparing two previously-sequenced bacterial genomes. BMC Genomics. 8:274.
    • (2007) BMC Genomics , vol.8 , pp. 274
    • Herring, C.D.1    Palsson, B.O.2
  • 23
    • 43549087573 scopus 로고    scopus 로고
    • Developing antibacterial vaccines in genomics and proteomics era
    • Kaushik, D.K., Sehgal, D. 2008. Developing antibacterial vaccines in genomics and proteomics era. Scandinavian Journal of Immunology. 67:544-552.
    • (2008) Scandinavian Journal of Immunology , vol.67 , pp. 544-552
    • Kaushik, D.K.1    Sehgal, D.2
  • 24
    • 37249056994 scopus 로고    scopus 로고
    • Declining wild salmon populations in relation to parasites from farm salmon
    • Krkosek, M., Ford, J.S., Morton, A., Lele, S., Myers, R.A., Lewis, M.A. 2007. Declining wild salmon populations in relation to parasites from farm salmon. Science. 318:1772-1775.
    • (2007) Science , vol.318 , pp. 1772-1775
    • Krkosek, M.1    Ford, J.S.2    Morton, A.3    Lele, S.4    Myers, R.A.5    Lewis, M.A.6
  • 26
    • 33747822277 scopus 로고    scopus 로고
    • REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes
    • Linke, B., McHardy, A.C., Neuweger, H., Krause, L., Meyer, F. 2006. REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Applied Bioinformatics. 5:193-198.
    • (2006) Applied Bioinformatics , vol.5 , pp. 193-198
    • Linke, B.1    McHardy, A.C.2    Neuweger, H.3    Krause, L.4    Meyer, F.5
  • 27
    • 42549149636 scopus 로고    scopus 로고
    • Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions
    • Mandel, M.J., Stabb, E.V., Ruby, E.G. 2008. Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: Focus on point miscalls and artefactual expansions. BMC Genomics. 9:138.
    • (2008) BMC Genomics , vol.9 , pp. 138
    • Mandel, M.J.1    Stabb, E.V.2    Ruby, E.G.3
  • 38
    • 48849091840 scopus 로고    scopus 로고
    • New ways to identify novel bacterial antigens for vaccine development
    • Movahedi, A.R., Hampson, D.J. 2008. New ways to identify novel bacterial antigens for vaccine development. Veterinary Microbiology. 131:1-13.
    • (2008) Veterinary Microbiology , vol.131 , pp. 1-13
    • Movahedi, A.R.1    Hampson, D.J.2
  • 39
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • Nagalakshmi, U., Wang, Z., Waern, K., Shou, C., Raha, D., Gerstein, M., Snyder, M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 320:1344-1349.
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 40
    • 43349084767 scopus 로고    scopus 로고
    • Scaffolding and validation of bacterial genome assemblies using optical restriction maps
    • Nagarajan, N., Read, T.D., Pop, M. 2008. Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics. 24:1229-1235.
    • (2008) Bioinformatics , vol.24 , pp. 1229-1235
    • Nagarajan, N.1    Read, T.D.2    Pop, M.3
  • 41
    • 84856609558 scopus 로고    scopus 로고
    • Trout Production
    • NASS
    • NASS. 2007. Trout Production. (http://usda.mannlib.cornell.edu/MannUsda/viewDocument Info.do?documentID=1172)
    • (2007)
  • 42
    • 18744383009 scopus 로고    scopus 로고
    • Aquaculture and ocean resources: Raising tigers of the sea
    • Naylor, R., Burke, M. 2005. Aquaculture and ocean resources: Raising tigers of the sea. Annual Review of Environmental Resources. 30:185-218.
    • (2005) Annual Review of Environmental Resources , vol.30 , pp. 185-218
    • Naylor, R.1    Burke, M.2
  • 46
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: Finding the elusive mis-assembly
    • Phillippy, A.M., Schatz, M.C., Pop, M. 2008. Genome assembly forensics: Finding the elusive mis-assembly. Genome Biology. 9:R55.
    • (2008) Genome Biology , vol.9
    • Phillippy, A.M.1    Schatz, M.C.2    Pop, M.3
  • 50
    • 39649084637 scopus 로고    scopus 로고
    • Bioinformatics challenges of new sequencing technology
    • Pop, M., Salzberg, S.L. 2008. Bioinformatics challenges of new sequencing technology. Trends in Genetics. 24:142-149.
    • (2008) Trends in Genetics , vol.24 , pp. 142-149
    • Pop, M.1    Salzberg, S.L.2
  • 51
    • 34147162107 scopus 로고    scopus 로고
    • Genome re-annotation: A wiki solution?
    • Salzberg, S.L. 2007. Genome re-annotation: A wiki solution? Genome Biology. 8:102.
    • (2007) Genome Biology , vol.8 , pp. 102
    • Salzberg, S.L.1
  • 52
    • 84885709306 scopus 로고    scopus 로고
    • Tools for gene finding and whole genome comparison
    • In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
    • Salzberg, S.L., Delcher, A.L. 2004. Tools for gene finding and whole genome comparison. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 19-31.
    • (2004) Microbial Genomics , pp. 19-31
    • Salzberg, S.L.1    Delcher, A.L.2
  • 55
    • 28944439470 scopus 로고    scopus 로고
    • Beware of mis-assembled genomes
    • Salzberg, S.L., Yorke, J.A. 2005. Beware of mis-assembled genomes. Bioinformatics. 21:4320-4321.
    • (2005) Bioinformatics , vol.21 , pp. 4320-4321
    • Salzberg, S.L.1    Yorke, J.A.2
  • 57
    • 46249095809 scopus 로고    scopus 로고
    • Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1
    • Silby, M.W., Levy, S.B. 2008. Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1. PLoS Genetics. 4:e1000094.
    • (2008) PLoS Genetics , vol.4
    • Silby, M.W.1    Levy, S.B.2
  • 58
    • 33745172816 scopus 로고    scopus 로고
    • History of microbial genomics
    • In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
    • Smith, H.O. 2004. History of microbial genomics. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 3-16.
    • (2004) Microbial Genomics , pp. 3-16
    • Smith, H.O.1
  • 60
    • 4344568000 scopus 로고    scopus 로고
    • Genome update: Annotation quality in sequenced microbial genomes
    • Ussery, D.W., Hallin, P.F. 2004. Genome update: Annotation quality in sequenced microbial genomes. Microbiology. 150:2015-2017.
    • (2004) Microbiology , vol.150 , pp. 2015-2017
    • Ussery, D.W.1    Hallin, P.F.2
  • 61
    • 38049076500 scopus 로고    scopus 로고
    • Bacterial genome annotation at TIGR
    • In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Humana Press, Totowa, NJ
    • White, O. 2004. Bacterial genome annotation at TIGR. In: Fraser, C.M., Read, T.D., Nelson, K.E. (eds), Microbial Genomics. Humana Press, Totowa, NJ, pp. 33-46.
    • (2004) Microbial Genomics , pp. 33-46
    • White, O.1


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