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IGEM Evry 2014

Biology - Genome Assembly

De novo Genome assembly

Assembly Strategy

In order to perform the genome assembly of our bacteria we choose to used the velvet software. We choose 4 kmer size. For the first one at 31 we obtained 1493 contigs. for a kmer size of 65, 413 contigs are obtain. For the two last kmer tested, 97 and 113 we obtained 275 and 245 contigs.The prokka software is an automated tools for genome annotation. The run take less than ten minutes, as they was proposed on their articles.In order to control the quality of our DNA seq we choose to made first a Proteome comparisons with Pseudovibrio FOBEG1 which is our reference strain. For that purpose we decided to look at our first genome version contains 275 contigs which was provide by the Velvet de novo assembly tools. For the 5456 proteins of Pseudovibrio FO-BEG1 5132 proteins (which are our reference strain) are match with a prokka anotation CDS. 5002 with a unique alignment 4936, 4687 with an alignement > 90%, 4415 > 95% and 2525 > 99%. For that purpose we are sure that we sequence a strain related to the Pseudovibrio genus. After this proteome comparison, we try to improved our genome assembly by improved the kmer size and we see that the contigs numbers was reduced to 245. In order to analyse the annotation and the quality of our genome annotation we look at 4 main specific annotation type such as antibiotic resitance, restriction enzyme, metals such as cadmium, copper and mercury, and other toxic compound such as phenol, nitrate, nitrite.

Antibiotic resistance

Restriction enzyme

Figure 1: Sequence of the pRhokHi vector and the hightlight of the EcoKI target sequence






Figure2 : Anaerobic pathway degradation for phenol