I am looking for a software that will allow to compare whole bacterial genomes to find conserved sequences. Ideally, the software should be capable for comparing several genomes and return list of genes annotated with some kind of conservancy factor.
Hi Marcin,
Have you tried the The Integrated Microbial Genomes (IMG)? It is an online platform that functions as "a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context."
Genome and metagenome datasets of bacterial, archaeal, eukaryotic, and phage genomes come from the NCBI’s Genbank/ RefSeq, and other set of publicly available metagenome samples. It contains some of the features you are looking for (e.g. under compare genomes: genome genes best homologs, genome clustering, etc.)
Here is the link just in case http://img.jgi.doe.gov/cgi-bin/w/main.cgi
IMG Content:
Datasets
Bacteria 4518
Archaea 182
Eukarya 187
Plasmids 1190
Viruses 2809
Genome Fragments 654
Total Datasets 9540
Last updated: 2012-12-04
Good luck!
Hi Marcin,
Have you tried the The Integrated Microbial Genomes (IMG)? It is an online platform that functions as "a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context."
Genome and metagenome datasets of bacterial, archaeal, eukaryotic, and phage genomes come from the NCBI’s Genbank/ RefSeq, and other set of publicly available metagenome samples. It contains some of the features you are looking for (e.g. under compare genomes: genome genes best homologs, genome clustering, etc.)
Here is the link just in case http://img.jgi.doe.gov/cgi-bin/w/main.cgi
IMG Content:
Datasets
Bacteria 4518
Archaea 182
Eukarya 187
Plasmids 1190
Viruses 2809
Genome Fragments 654
Total Datasets 9540
Last updated: 2012-12-04
Good luck!
Hi Rolando!
It looks like that's the thing I am looking for.
What I need exactly is to find a gene or couple of genes that are homologous (for a group of species) and retrieve their sequences for further analysis. Does IMG has such feature or I need to do some of the work manually?
I have used the "Find Genes" tab - - Phylogenetic Profilers -- "Single Genes" to find genes gained by pathogenic strains which is the opposite of what you want. However, if you select one genome in the column "find genes in*" and them a group of genomes from the column "with homologs in" and then,- - modify the E value as stringent as you want, "Exclude pseudogenes", modify the "Min. Percent of identity", etc (at the bottom of the page - irt runs a BLASTP. From the results table, select the gene of interest, click on its "Gene Object ID" to see more details and even Customize the homolog display at the bottom of the Gene page.
I would like to see other researchers' approach to this problem.
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