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AnnotationPipeLine

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2005-12-03

Annotation Pipe Linea

YearCenterAssemblGene FindHomologyDBDomainEtc
1995Haemophilus influenzae RdTIGRAUTOASSEMBLER, TIGR ASSEMBLERGENEMARKBLAZE, PRAZENRBP*1-inter genic sequences v.s. SwissProt?, PIR, GenBank?
2005-07-25Pelagibacter ubique SAR11 HTCC1062Oregon State Univphred, phrap, consed, autofinishGlimmer2.13BLASTPSwissProt?, alphaproteobacteria-protein, NCBI-nraaPfam, InterPro?, TMHMMGenDB, PyPhy?*2
2005-10-03Streptococcus agalactiae A909TIGRCeleraAssembler?, PROMER(contig order)Glimmer
2005-07-26Colwellia psychroerythraea 34HTIGRMethe´, B. A. et al. (2003) Science 302, 1967–1969.
15. Heidelberg, J. F. et al. (2004) Nat. Biotechnol. 22, 554–559.		Glimmer*3 >30a.a.nraa*4DBTOPPRED (17). The 5'regions of eachORFwere inspected to define initiation codons using homologies, position of ribosomal binding sites, and transcriptional terminators. Two sets of hidden Markov models were used to determine ORF membership in families and superfamilies:PFAM 14.0 (18) and TIGRFAMs 4.0 (19). PFAM 14.0Etc
2005-04-06Chlamydophila abortus S26/3SangerAssembl*5Gene FindHomologyDBSignalP, HMMER, ...Artemis
2004-10-04Nocardia farcinica IFM 10152NIID, Kitasato Univ, Chiba Univphred, phrapglimmer, blast, FLAMEPLOT, tRNAscan-SEGCGblastclust; a minimum of 30% identity and 70% length coverage.
2004-12-08Geobacillus (Bacillus) kaustophilus HTA426JAMSTEC14. Kunst,F. et al. (1997) The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature, 390, 249–256.
15. Takami,H. et al. (2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res., 28, 4317–4331.
16. Takami,H. (2002) Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments. Nucleic Acids Res., 30, 3927–3935.		Gene FindHomologyDBDomainEtc
2003-12-14Rhodopseudomonas palustris CGA009Joint Genome Institute
Institute of Molecular Genetics, Prague		phred, phrap, consedCritica, Glimmer, GenerationBLASTP >= 50% aa identify & > 80% length of matchNCBI-nraa, KEGG GenesInterPro? >= 30aa, > 80%Etc

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*1 Non redundant bacterial protein:from GenBank?, SwissProt?
*2 To detect instances of horizontal gene transfer the program PyPhy? was used to investigate phylogenetic relationships to nearest neighbors for all genes
*3 trained with ORFs < 90bp the genomic sequence that had BLASTX hits to The Institute for Genomic Research nonredundant internal protein database with an expectation value better than 1x10^-5 was well as with any C. psychrerythraea genes available in GenBank?.
*4 Methe´, B. A., Nelson, K. E., Eisen, J. A., Paulsen, I. T., Nelson, W., Heidelberg, J. F., Wu, D., Wu, M., Ward, N., Beanan, M. J., et al. (2003) Science 302, 1967–1969.
*5 Parkhill, J., Achtman, M., James, K.D., Bentley, S.D., Churcher, C., Klee, S.R., Morelli, G., Basham, D., Brown, D., Chillingworth, T., et al. 2000. Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404: 502–506.