Genome homology tool comparing two distance species

Question

[Chris]

Hello,

I'm looking for a genome homology tool that will be able to compare two different insect species' genomes and identify whether or not each base is in a homologous region in the other genome. I'd like the output show both genomic locations.

Eg.

>chr1 insect A
GCCTAAGTCG

>chr1 insect B
GCCAAGTAAAACG

GCCTAAGT----CG

GCC-AAGTAAAACG

chr1 insect A 1   = chr1  insect B 1 

chr1 insect A 2   = chr1  insect B 2

chr1 insect A 3   = chr1  insect B 3 

chr1 insect A 5   = chr1  insect B 4 

chr1 insect A 6   = chr1  insect B 5 

chr1 insect A 7   = chr1  insect B 6 

chr1 insect A 8  = chr1  insect B 7 

chr1 insect A 9  = chr1  insect B 12 

chr1 insect A 10   = chr1  insect B 13

The best way I can think to do this is to use a tool like Minimaps to generate a sam file, then use samtools mpileup to get each genomic location. But I think that by doing this I will lose the chromosomal positions for my second organism.

Does anybody have any advice?

Thanks in advance.

Answer 1

[colindaven]

Use minimap2 with paf file output to retain the mapping information in both genomes.

JBrowse2 has a synteny feature which should be able to read the two genomes and the mapping paf file between them if you're lucky.

Answer 2

[SanjidaR_NCBI]

Hi! NCBI has a Comparative Genome Viewer (CGV) (https://www.ncbi.nlm.nih.gov/cgv) that shows comparisons between two complete euk genomes.

There are a lot of insect genome comparisions there already, e.g. https://www.ncbi.nlm.nih.gov/cgv/browse/GCF_009650485.2/GCF_000001215.4/40865/7291

The viewer doesn't zoom to sequence, but you can zoom into your region of interest and then find an option to View alignment sequence in the right-click menu.

You can also use the links or right-click menu option from CGV to go to the NCBI GDV genome browser and view the assembly alignment as a browser track. The GDV browser zooms to sequence level, so you can compare sequence from there.

You can use the feeback buttons on CGV to contact NCBI to request alignments between genomes and if you need help with anything.

[GenoMax]

This tool allows you to compare two genomes based on assembly-assembly alignments provided by NCBI.

So this tool can only be run on NCBI's genomes correct? OP is likely asking for a tool that will work with their own genomes. Or is CGV available for download? It may be a cool tool to release publicly, if it does not depend on specific NCBI infrastructure.

[SanjidaR_NCBI]

Sorry for the delay - don't have notifications on. Yes, CGV only shows pairwise alignments we provide, though we can create an alignment between euk assemblies on request. We're not currently planning to make CGV public in the near future.

So, our team is currently working on a multiple alignment viewer which will display user analysis, e.g. Cactus alignments or similar. We hope to have a beta out by the end of the year. Follow NCBI's lists (https://ncbiinsights.ncbi.nlm.nih.gov/ncbi-rss-feeds-listservs/) or on LinkedIn to get an announcement.