F.A.Q.
- How Do I Cite Pogo?
- Can I add the same genome to both group A and group B?
- Why are my results missing some of the genome pairs I queried?
- Why are some metrics missing for a few pairs of genomes?
- What does the option Calculate Average Ranking” do?
- Why do you provide two criteria for determining orthologs?
- Why does the database only cover genome pairs whose 16S rRNA identity is above 80%?
- Why does the database provide branch selection only up to the genus level?
- Can I download the entire database?
- Can I download all the raw BLAST results?
- Can I download the sequences of all orthologs between each pair of genomes?
How Do I Cite Pogo?
Can I add the same genome to both group A and group B?
Yes. Users may sometimes add a genome to group A twice or group B twice, for example, one may add genome “Escherichia_coli_042_uid161985” to group A, and then add the entire species “Escherichia coli” to group A. In such cases, we will only keep a unique list of the genomes in a group. POGO-DB also allows users to add a genome to both group A and group B, however, the comparison between exactly the same genome will not show up (since all metrics will be 100% similar when comparing a genome to itself). If users want to compare genomes pairwisely within a group of genomes, say a species or genus, they can either add the same genomes to both group A and B for comparison, or add them only to group A and select “Compare A to itself” before submitting the query.
Why does the result missing some of the genome pairs I queried?
The POGO-DB contains BLAST result of pairs of genomes whose 16S rRNA identity is above 80%, therefore some pairs of genomes may not be returned if the pair does not meet this criterion. The reason that we apply such a limitation is because the BLAST between genomes is a very time consuming computation. The 717,861 bi-directional genome-wise BLAST took 150+k CPU hours. Besides, the major aim of the database is to provide information on marker gene selections for finer taxonomic levels, while many known marker genes (primarily the 16S rRNA gene) already provide satisfactory distinction at higher taxonomic levels. There are two other reasons that the result page may not provide all combination of pairs of genomes selected. For one, we are not showing the result for comparing a genome to itself because all metrics will be 100% similar. The second reason may be that users did not check the option “Compare A to itself” or “Compare B to itself”, and therefore will only see the default comparison between genomes in group A vs. genomes in group B.
Why are some metrics missing for a few pairs of genomes?
The POGO-DB only computes the average AAI if two genomes have at least 200 orthologs (as defined by criterion 1). Similarly, genomic fluidity is only computed for genomes with at least 200 orthologs (as defined by criterion2). The limitation prevents us from quantifying the overall genomic similarity based on only a few genes. The database also provides the identity of 73 marker genes, which are identified via BLAST search for each genome. Although each marker gene is found to be present in over 90% of the genomes, there are still some genomes that do not contain the gene. Therefore, pairs of these genomes will not have the identity of some marker genes.
What does the option "Calculate Average Ranking" do?
In addition to the several metrics we provide for each genome pair, we also allow users to compare the evolution rate of marker genes relatively to each other. The average rank is such a metric we applied for this purpose. You can find our explanation of this metric here. Briefly, we rank the marker genes (including the 16S rRNA gene) by their identities between each pair of genomes, and then take the average rank of each gene across all pairs of genomes. The ranking of marker genes will only be computed for pairs of genomes where all marker genes are identified in both genomes.
Why do you provide two criteria for determining orthologs?
We used criterion1 (70+% read length covered with 30+% identity at the amino acid level) to define orthologs used for computing the average AAI between two genomes. This is the same criterion used by Konstantinidis and Tiedje. However, the genomic fluidity is a metric for quantifying genes unique to a genome rather than the orthologs shared by both genomes. Therefore, in order to be stricter about calling a gene unique to a genome, we applied a second and loosened criterion for defining orthologs. Hence the computation of genomic fluidity is more reliable than using the same criterion as the computation of average AAI.Why does the database only cover genome pairs whose 16S rRNA identity is above 80%?
The reason that we apply such a limitation is because the BLAST between genomes is a very time consuming computation. The 717,861 bi-directional genome-wise BLAST took 150+k CPU hours. Besides, the major aim of the database is to provide information on marker gene selections for finer taxonomic levels, while many known marker genes (primarily the 16S rRNA gene) already provide satisfactory distinction at higher taxonomic levels. To view which pairs of genomes are included in the database and which are not, please download the 16S rRNA percent identity table of all genomes pairwisely here POGODB_16S_rRNA_identity.csv.bz2
Why does the database provide branch selection only up to the genus level?
The search time will increase exponentially to the number of genomes queried. Therefore, we encourage users to add genomes by species or genera to the query. For people who are interested in the comparison between more or all of the genome pairs, we encourage them to acquire all the information in the database or view some of the all genomes vs. all genomes results on our about page.
Can I download the entire database?
Yes. In addition to the download link we provided every time for the selected genomes in one query, users can acquire the entire database including both the identity information ( POGODB_all_genome_pairs_identities.csv.bz2), and the all of the BLAST output files ( All.tar). We encourage users to do so when they are interested in a large amount of genome pairwise comparisons.
Can I download all the raw BLAST results?
Yes. In addition to the download link we provided for the queried genome pairs, we also allow users to download the raw BLAST output files for all pairs of genomes we provided. This is in fact one of the major reasons we built this database: to save people from the massive computation time of BLAST-ing genomes against genomes. It should be noted that we have BLAST results for a total of 717,861 pairs of genomes, bi-directionally. Therefore, the final output takes approximately 680G’s storage (bz2 compressed) and will take a long time to download.
Can I download the sequences of all orthologs between each pair of genomes?
Yes. In addition to the whole genome BLAST files we provided for download (for user selected comparisons or all comparisons), users will get a list of gene ID indexing upon download. This indexing file could be used to map each gene ID in the BLAST files to the accession number plus gene location in the NCBI database. Users can therefore download the sequences for their downstream analyses.