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Old 09-14-2012, 07:34 AM   #1
mm.perrineau
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Location: New Jersey

Join Date: Sep 2012
Posts: 12
Question How compare together 3 partial genomes?

Hi everybody,

First, I just begin a new post-doc and i never never do some genomic (or transcriptomic) before.
And in my lab, the bioinformatic guys don't have the time to help me.
So, i will learn everything by myself...

My problem is I have to compare 3 seaweed genomes (3 strains from the same species).
They have been sequence by Illumina MiSeq...
Each are composed by 3000 to 5000 contigs.
The contigs are between 200 and 63 000-130 000 pb.
The lenght total are between 19.25 Mbp and 19.45 pb.
Nobody know the size of the genome !!!
A old paper said, this species have propably 8 to 10 chromosomes + 1 mitochontriome + 1 chloroplaste
And, there is not reference genome to help me.

My question is :
Do you know some solfwares to help me to try to align, to compare those 3 genomes?
I would like to have a global idea, if I have pratically the complet genome or if we need to make more sequencing run.
I would like to have an idea, if I have lot of unique element in each one genome... vern diagramm...
And probably other informations that i don't kown...


I will probably, in the futur weeks ask too for some good annotation genome softwares for eukaryote
and for SNPs detection, sequence insertion detection...
and lot of "classic analysis" possible to compare genomes !!!!!

THANK YOU SO MUCH !!!!!

Marie-Mathilde
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Old 09-19-2012, 09:53 AM   #2
chkuo
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You can start with a genome alignment (e.g., MAUVE) to see if you can align the large contigs. If you want to use a Venn diagram to show the share/unique, then you probably need to have gene prediction first and run ortholog clustering (e.g., OrthoMCL/TribeMCL).
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Old 10-09-2012, 03:30 AM   #3
gaffa
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One thing you can do to get a general overview is to make pairwise dot-plots of the assemblies, using for example the mummerplot program from the MUMmer package (http://mummer.sourceforge.net/). The output looks something like this (where a diagonal line indicates a stretch of similarity between two chromosomes/contigs/scaffolds of the two different assemblies):

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Old 12-11-2012, 01:53 PM   #4
mm.perrineau
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Thank you !!!
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