I need to make a comparison of two large genomes of very similar organisms. Is there any software capable of visualizing the exact positions that vary in alignment? It's too difficult to look through the whole alignment of GB-size genomes. I would be grateful for any suggestions.
As many people mentioned, LASTZ is a good option (http://www.bx.psu.edu/~rsharris/lastz/). Then you can run variscan (http://www.ub.edu/softevol/variscan/) which can give you some nice statistics/comparisons between the genomes. Or you can just view LASTZ maf alignment in gmaj (http://globin.bx.psu.edu/dist/gmaj/) and look for differences there.
There are several genome alignment softwares around. For a fist pass, LAST gives a nice and simple output: www.last.cbrc.jp.
Double-ACT is for circular bacterial genomes, typically 2 to 10 megabases in size. I think you are looking for something else, but I thought I'd drop the double-ACT suggestion here for other people who might come to this discussion looking to compare bacterial genomes.
http://www.hpa-bioinfotools.org.uk/pise/double_act.html
As already suggested, LAST might be an option for you. It is quite fast and produces decent pairwise alignments. You can also try to run Progressive Cactus (incorporates lastz in the alignment process).
What kind of data do you have? If you have NGS data, you could map the reads from one species 1 to the genome/assembly of species 2 and do variante calling (e.g. using SAMtools, GATK).
First of all you need to align both to a reference genome using one of different tools existing depending on the size of genome sequence repeats and type of libraries you have I attached a link for you "most cases you will use bowtie2" . after mapping you will have two sam or bam files contains the mapped reads two compare two genomes I think you need to know the copy number variation deletion insertion SNP .... etc, there is other tools that you will use where the input will be the mapping file from step one and the reference tools are "Pindel and Dindel" , then you will have files for the changes in both genomes that you can track by visualizing them ether in IGV or "and I encourage to use " Savant.
Good luck
http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)/Alignment#Mapping_algorithms
Dear sir,
You can compare between the two genomes by RAPD techniqe to see bands only.but if you want see the differences in sequences between two genomes is immposible.but you can seperate I
As many people mentioned, LASTZ is a good option (http://www.bx.psu.edu/~rsharris/lastz/). Then you can run variscan (http://www.ub.edu/softevol/variscan/) which can give you some nice statistics/comparisons between the genomes. Or you can just view LASTZ maf alignment in gmaj (http://globin.bx.psu.edu/dist/gmaj/) and look for differences there.
May be by restriction analysis of the two genome. If you have fund you can compere by sequencing
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