Category: Annotation Data
 
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document.png P.aeruginosa CCBH4851 assembly HOT

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 The assembly was done using the hybrid assembler MaSuRCA (http://www.genome.umd.edu/masurca.html). The inputs were reads from Illumina (300 cycles and 500 cycles) and PacBio platforms. The combination of Illumina and PacBio reads generated a single contig that, after careful analysis, was adopted to represent the genome of the CCBH4851 strain.


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document.png P.aeruginosa CCBH4851 annotation HOT

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The annotation was made using a set of protocols. First, annotation of genes exhibiting homology with PAO1 (NC_002516), PA7790 (NZ_CP014999), PA11803 (NZ_CP015003) strains was transferred to CCBH4851 using the RATT program (http://ratt.sourceforge.net). Predictions were made with the GenemarkS (http://exon.gatech.edu/GeneMark) and Glimmer (https://ccb.jhu.edu/software/glimmer) programs, and the ORFs that were left unmarked were submitted to BLASTp searches and were annotated accordingly. Predictions for rRNA and tRNA were also made with the RNAmmer programs (http://www.cbs.dtu.dk/services/RNAmmer) and tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE ), respectively. Discrepant annotations, e.g. ORFs detected or transferred in the same region but with different transcription directions, were analyzed individually and manually, through BLASTp searches and queries to conserved protein domain databases, taking into account the most significant results (identity, greater number of homologues, conserved domains, experimental evidence) and also the genetic context depending on the known function of neighboring genes. Finally, to designate an EC number for annotated proteins, the PRIAM program (http://priam.prabi.fr/REL_MAR15/index_mar15.html) was used and only EC numbers detected with probability greater than 0.9 were assigned to the respective proteins.



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