I have 2 bacterial genome sequences- i.e draft genomes. The genus are the same, but to discriminate on species level, what tools can I apply? There are a set of genes similar in both strains and some are unique, but that could be the sequencing gaps as it is not a whole complete genome sequenced, how do I make sure the strains are not the same and on what basis can I prove the difference?
The standard method is to compare the 16S rRNA gene sequences between the two strains if they are more than 1 - 1.5% divergent they are usually considered diferent species. You should also compare percent GC content as this tends to be very species-specific. Other methods include those based on core genome effects. If you have an established core genome for a species and if you add a strain to that analysis and it results in a 5% or more decrease in the size of the core genome that is also a crtierion for identfying it as another species.
The standard method is to compare the 16S rRNA gene sequences between the two strains if they are more than 1 - 1.5% divergent they are usually considered diferent species. You should also compare percent GC content as this tends to be very species-specific. Other methods include those based on core genome effects. If you have an established core genome for a species and if you add a strain to that analysis and it results in a 5% or more decrease in the size of the core genome that is also a crtierion for identfying it as another species.
It depends. Does your genomes very fragmented or you have few contigs for both genomes? If you have few contigs is very difficulty (not impossible) that the unique genes are result from the sequencing gaps. Moreover, you can't look to the end of the contigs (the more problematic region). MUMmer is a good suggestion. In addition you can align the both genomes using Mauve (http://gel.ahabs.wisc.edu/mauve/).
The more important question may be quality control and validation of your draft genomes. Do they have a relative with a published genome that can be mapped to?
You have two bacterial draft genomes. Are they assembled? If not, you can use Newbler (Miller et al., Genomics 95:315-327, 2010), MIRA 3 (Chevreux et al., Genome Res. 14:1147-1159, 2004) or a couple of other programs to assemble them depending on sequencing platform used. For genome analysis you can use different platforms like Rapid Annotation Server (RAST; http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/RapidAnnotationServer).We are developing the bioinformatics platform MEGGASENSE: the metagenome/genome annotated sequence natural language search engine. This platform is not jet published but we can help you if you have an interest ([email protected]). For genome comparison you can use MUMmer (Kurtz et al., Genome Biology 2004, 5:R12) program to rapidly aligning entire genomes, whether in complete or draft form. MUMmer is also implemented in MEGGASENSE.
Up load sequences on RAST server. It will give nearest neighbour based on WGS. Only limitation is comparision will be made with available bacterial WGS!
yes Chaitanya Joshi I have uploaded the 2 genomes .........on RAST but it does not give a conclusion on the difference in genomes is if based on actual difference or difference in sequencing and gaps generated .!
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