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Pipeline publication

[…] in the sequence were primarily identified by mate-pair sequences and then closed by primer walking on gap-spanning library clones or genomic DNA amplified PCR products. True physical gaps were closed by combinatorial and multiplex PCR. All repeated sequences were addressed using mate-pair sequences and PCR data. Sequence finishing and polishing added 638 reads. The final assembly of the main chromosome and 3 plasmids from 84,830 reads produced approximately 13-fold coverage across the genome. Assessment of final assembly quality was completed as described previously []., Automated gene prediction was completed by assessing congruence of gene call results from three independent programs, the Critica [], Generation, and Glimmer [] modeling packages, and by comparing the translations to the GenBank nonredundant database using the basic local alignment search tool for proteins (BLASTP). Product description annotations were obtained using searches against the KEGG, InterPro, TIGRFams, PROSITE, and Clusters of Orthologous Groups of protein (COGs) databases. The tRNAScanSE tool [] was used to find tRNA genes, whereas ribosomal RNAs were found by using BLASTN vs. the 16S and 23S ribosomal RNA databases. Initial comparative analyses of bacterial genomes and gene neighborhoods were completed using the JGI Integrated Microbial Genomes web-based interface (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi). Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform (http://img.jgi.doe.gov/er) []., The gen […]

Pipeline specifications

Software tools CRITICA, Glimmer, BLASTN, BLASTP
Databases TIGRFAMs