IMG User Scenario February11, 2011
IMG/M User Tasks List
A. Using Genome Browser and Metagenome Details
1. How many metagenomes are there in IMG/M?
2. How many bins are there in Acid Mine Drainage metagenome?
3. To which phyla the proteins in Acid Mine Drainage metagenome have
the highest number of hits?
4. How many scaffolds in Acid Mine Drainage metagenome have GC
content below 30%?
5. Using Phylogenetic Profiler on Microbiome Details page, find how
many genes with COG hits are present in Methylococcaceae bin of
Lake Washington (combined v2) metagenome, but not in the genome
of Methylococcus capsulatus.
B. Using Phylogenetic Distribution of Genes and Scaffold Cart
1. How many genes in Sludge/US, Phrap Assembly metagenome have
the best hit to Alphaproteobacteria with percent identity between 60 and
90%?
2. How many genes in Sludge US Phrap metagenome with the best hit to
Alphaproteobacteria at 60-90% identity belong to the COG Functional
Category of “Amino acid transport and metabolism”?
3. Which family of Betaproteobacteria has the highest number of best
hits from the genes in Sludge US Phrap metagenome (cumulative
above 30% identity)?
4. Which archaeal genome has most hits with >90% identity from the
metagenomes of human gut subject 7 and human gut subject 8?
5. What are the functions of genes in the region between 270 kb and 330
kb of isolate Methanobrevibacter smithii that are missing from
Methanobrevibacter smithii from human gut subject 7 metagenome?
IMG User Scenario February11, 2011
Are these genes also absent from Methanobrevibacter smithii from
human gut subject 8 metagenome?
6. What is the range of GC content of contigs assigned to the bin
“Accumulibacter” (binning method PhyloPythia) in Sludge US Phrap
metagenome? What is the range of read depths for this bin?
C. Using Find Functions
1. Which Pfams describe carbohydrate-binding modules (CBM)?
2. Are there any CBM-containing genes in human gut subject 7 and
subject 8?
3. Do A. phosphatis bins in Sludge/Australian, Phrap Assembly and
Sludge/US, Jazz Assembly metagenomes have all COGs assigned to
“Histidine biosynthesis” pathway? Do they have a complete pathway?
4. Representatives of which phyla are likely to be present in the
metagenome of human gut community subject 7 when COG0200
(Ribosomal protein L15) is used?
D. Using Find Genes
1. Which domains are associated with carbohydrate binding module
family 6 (CBM_6, pfam03422) in Soil microbial communities from
Minnesota farm metagenome?
E. Using Compare Genomes
1. Using Abundance Profile Search, find, how many Pfams are at least
twice as abundant in the metagenome of human gut community
subject 7 as compared to human gut community subject 8 using
frequency normalization. Which Pfam has the highest frequency in
human gut community subject 7 metagenome? Is it more abundant
than in human gut community subject 8 metagenome by frequency?
By raw counts?
2. Using Function Comparisons, find which COG is most
overrepresented in the metagenome of human gut community subject
7 as compared to human gut community subject 8. Is this result
IMG User Scenario February11, 2011
statistically significant? Which COGs are significantly
overrepresented in human gut community subject 7 as compared to
human gut community subject 8? Use D-score as statistic and gene
count.
3. Using Function Category Comparisons, find which COG Pathways
are overrepresented with p-value less than 1.0e-01 in human gut
subject 7 metagenome as compared to human gut subject 8
metagenome. How these results could be interpreted with respect to
the overrepresentation of individual COGs in the same metagenome?
4. Using Genome Clustering, find, which of 5 mouse gut community
metagenomes are the closest according to their COG frequency
distributions? According to their Pfam frequency distribution?
5. Using Phylogenetic Distribution, find, which phyla are
underrepresented in metagenomes of 2 obese mice as compared to 3
lean mice using “Gene count” and BLAST hits with identity above
60%. Which phyla are overrepresented?
F. Using SNP BLAST and SNP VISTA.
1. Using SNP BLAST and SNP VISTA find whether there are any
populations within Leptospirillum sp. group II bin of Acid Mine
Drainage metagenome.
2. Is there any evidence of recombination between populations within
Ferroplasma acidarmanus type I bin of Acid Mine Drainage
metagenome?