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Old 05-31-2012, 05:16 PM   #1
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Location: Australia

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Default 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.

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Old 06-01-2012, 12:53 AM   #2
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Maybe InParanoid can help you? From the documentation

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.
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Old 06-01-2012, 02:17 AM   #3
Location: UK

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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.

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Old 06-01-2012, 09:54 AM   #4
Location: Raleigh, NC

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A clutering tool like cd-hit would work.
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Old 06-02-2012, 08:56 AM   #5
Location: RTP, NC, USA

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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.
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Old 03-04-2014, 07:36 AM   #6
Location: Montreal

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Hi, I'm facing the same kind of situation. Anybody here used InParanoid successfully?
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Old 03-04-2014, 03:03 PM   #7
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Muave generates visual comparisons for genomes.

BTW: Are you not able to make InParanoid work?
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Old 03-05-2014, 10:19 AM   #8
Location: Montreal

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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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genes diversity

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