About tools for comparing genomes of two different organisms

v3borg · 05-31-2012, 05:16 PM

Hi Bioinformatics gurus,

Could you suggest me any tool(s) for comparing genomes of two (or more) different organisms to have at the end a list of genes of organism A which are lacking in organism B? And also, a list of common genes in both organisms which are drastically different.

Thanks

dariober · 06-01-2012, 12:53 AM

Maybe InParanoid http://www.ncbi.nlm.nih.gov/pubmed/19892828 can help you? From the documentation http://inparanoid.sbc.su.se/download...t/relnotes.txt

Quote:

1. Introduction

InParanoid is a program for automatic identification of orthologs
while differentiating between inparalogs and outparalogs. An
InParanoid cluster is seeded by a reciprocally bestmatching ortholog
pair, around which inparalogs are gathered independently, while
outparalogs are excluded. The InParanoid database is a collection of
pairwise ortholog groups aiming to include all 'completely sequenced'
eukaryotic genomes. By this we mean above 6X coverage, and less than
1% X letters in the protein sequences.

Raj · 06-01-2012, 02:17 AM

Hi,
I'm assuming they've been annotated and are bacteria/virus.
You can use MAUVE, which can do the alignment of 2 or more genomes and there is an option output orthologues based on your cutoffs. The output is a table (which can be opened in excel), where across the top (X axis) are the organism name, below which are the genes present. Comparing the columns, you can pull out whats shared and whats not.

Alternatively, you could you Blast to compare and pull out similar sequences between the genomes, again using what ever cutoff you like - that can be the more labour intensive way and gets complicated with 3 or more genomes.

Cheers,
Raj

Mark · 06-01-2012, 09:54 AM

A clutering tool like cd-hit would work.

jmw86069 · 06-02-2012, 08:56 AM

No second dariober's suggestion to use InParanoid. Its summary information and definitions of orthologs vs paralogs is quite useful. The key is that you must have annotated organisms to start with. And keep in mind the most likely differences are going to arise from genome assembly errors. For example my first pass filter on gene loss is to run peptide BLAT/BLAST and look for hits on the *_random chromosomes. I'd often find fragments of the gene at the edges of genome gaps. Sometimes half the gene would be on chr6, the other half on chr6_random, but you could see pretty much anything, depending upon the quality of the assembly and the annotation. But InParanoid should in theory help you figure out what to follow up with a deeper analysis, ie what holes there are to fill.

Birdman · 03-04-2014, 07:36 AM

Hi, I'm facing the same kind of situation. Anybody here used InParanoid successfully?

GenoMax · 03-04-2014, 03:03 PM

Muave generates visual comparisons for genomes.

BTW: Are you not able to make InParanoid work?

Birdman · 03-05-2014, 10:19 AM

Thanks GenoMax, I'm now trying Mauve. As for InParanoid, I'm not able to make it work on my transcriptomes. It's working with a small subset of sequences (a few thousands sequences) but it freezes forever when I try with the whole transcriptomes (hundreds of thousands sequences).

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05-31-2012, 05:16 PM	#1
v3borg Junior Member Location: Australia Join Date: May 2012 Posts: 1	About tools for comparing genomes of two different organisms Hi Bioinformatics gurus, Could you suggest me any tool(s) for comparing genomes of two (or more) different organisms to have at the end a list of genes of organism A which are lacking in organism B? And also, a list of common genes in both organisms which are drastically different. Thanks

06-01-2012, 02:17 AM	#3
Raj Member Location: UK Join Date: Jan 2009 Posts: 15	Hi, I'm assuming they've been annotated and are bacteria/virus. You can use MAUVE, which can do the alignment of 2 or more genomes and there is an option output orthologues based on your cutoffs. The output is a table (which can be opened in excel), where across the top (X axis) are the organism name, below which are the genes present. Comparing the columns, you can pull out whats shared and whats not. Alternatively, you could you Blast to compare and pull out similar sequences between the genomes, again using what ever cutoff you like - that can be the more labour intensive way and gets complicated with 3 or more genomes. Cheers, Raj

06-01-2012, 09:54 AM	#4
Mark Member Location: Raleigh, NC Join Date: Nov 2008 Posts: 51	A clutering tool like cd-hit would work.

06-02-2012, 08:56 AM	#5
jmw86069 Member Location: RTP, NC, USA Join Date: Jun 2009 Posts: 28	No second dariober's suggestion to use InParanoid. Its summary information and definitions of orthologs vs paralogs is quite useful. The key is that you must have annotated organisms to start with. And keep in mind the most likely differences are going to arise from genome assembly errors. For example my first pass filter on gene loss is to run peptide BLAT/BLAST and look for hits on the *_random chromosomes. I'd often find fragments of the gene at the edges of genome gaps. Sometimes half the gene would be on chr6, the other half on chr6_random, but you could see pretty much anything, depending upon the quality of the assembly and the annotation. But InParanoid should in theory help you figure out what to follow up with a deeper analysis, ie what holes there are to fill.

03-04-2014, 07:36 AM	#6
Birdman Member Location: Montreal Join Date: Jan 2014 Posts: 21	Hi, I'm facing the same kind of situation. Anybody here used InParanoid successfully?

03-04-2014, 03:03 PM	#7
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Muave generates visual comparisons for genomes. BTW: Are you not able to make InParanoid work?

03-05-2014, 10:19 AM	#8
Birdman Member Location: Montreal Join Date: Jan 2014 Posts: 21	Thanks GenoMax, I'm now trying Mauve. As for InParanoid, I'm not able to make it work on my transcriptomes. It's working with a small subset of sequences (a few thousands sequences) but it freezes forever when I try with the whole transcriptomes (hundreds of thousands sequences).