Example output¶
This section contains some examples of what the output of TCUP looks like. TCUP can output results in several formats.
Taxonomic composition¶
The main output format intended for human consumption for taxonomic composition
estimation is xlsx, i.e. Microsoft Excel format. The Excel file is not
produced by default, and has to be requested on the command line using
--write-xlsx XLSX_FILE. The Excel output contains two sheets: Taxonomic
composition and Hits to annotated regions. These two outputs are described
in detail below.
Taxonomic composition¶
A summary table of all discriminative peptide assignments are listed in this sheet. The output can look like this (shortened for brevity):
Cumulative Discriminative count Percentage Rank Description
921 738 98.29% genus Streptococcus
953 32 97.94% family Streptococcaceae
171 157 94.34% species Streptococcus pneumoniae
7 7 25.93% no rank Streptococcus pneumoniae 70585
5 5 18.52% no rank Streptococcus pneumoniae CGSP14
2 2 7.41% no rank Streptococcus oralis Uo5
1 1 3.70% no rank [Eubacterium] eligens ATCC 27750
1 1 3.70% no rank Campylobacter concisus 13826
1 0 3.70% no rank Clostridiales incertae sedis
1 1 3.70% no rank Mycobacterium rhodesiae NBB3
[...]
The columns, from left to right, are:
Cumulative: The number of discriminative fragments at the reported Rank. These figures also include all peptides below the indicated Rank (hence Cumulative).Discriminative count: The number of discriminative peptides only at the indicated Rank. This figure does not include peptides on any other Rank.Percentage: The proportion of all discriminative peptides at the indicated Rank that belong to this identification. Note that these numbers are only comparable within a given Rank; i.e. the sum to 100% within each Rank and have no meaning when comparing two different ranks.Rank: The rank at which peptides were discriminative.Description: The strain, species, genus, family, etc.
Looking at the results displayed above, we can see that this sample most likely contains Streptococcus pneumoniae, as indicated by the strong signal at species level (94.34%). This is further strengthened by the strong indicators at both genus and family level. In this shortened output we see some peptides that were discriminative to different strains of S. pneumoniae, but also two peptides discriminative to S. oralis. Towards the end of the output, several spurious matches to organisms that were probably not in the sample are also visible.
When viewing the output in Microsoft Excel, it is possible to use the filtering
tools to filter e.g. the Rank column on species to display only the
results on species level. This makes it very easy to study the results in
detail, depending on whatever question is most interesting to you.
Note
The taxonomic composition output can also be written to a text file,
using the --output command line option. If this option is not used,
this output is printed to STDOUT.
Hits to annotated regions¶
Results in the Hits to annotated regions sheet are somewhat harder to interpret than the results in the Taxonomic composition sheet. In this sheet, the output might look like this (shortened for brevity):
Species Disc. level Count Product Features
Streptococcus pneumoniae AP200 family 151 hypothetical protein ID=cds741;Name=YP_003876344.1;Parent=gene747;Note=Operon 340 Gene 1 protein supported gi%7C148997148%7Cref%7CZP_01824802.1%7C ribosomal protein S16;Dbxref=Genbank:YP_003876344.1,GeneID:9726765;gbkey=CDS;product=hypothetical protein;protein_id=YP_003876344.1;transl_table=11
Streptococcus pneumoniae R6 genus 96 hypothetical protein ID=cds26;Name=NP_357627.1;Parent=gene36;Dbxref=Genbank:NP_357627.1,GeneID:933816;gbkey=CDS;product=hypothetical protein;protein_id=NP_357627.1;transl_table=11
Streptococcus pneumoniae CGSP14 genus 81 hypothetical protein ID=cds32;Name=YP_001834750.1;Parent=gene38;Dbxref=Genbank:YP_001834750.1,GeneID:6216513;gbkey=CDS;product=hypothetical protein;protein_id=YP_001834750.1;transl_table=11
Streptococcus pneumoniae ST556 genus 78 hypothetical protein ID=cds106;Name=YP_006252305.1;Parent=gene112;Dbxref=Genbank:YP_006252305.1,GeneID:12900645;gbkey=CDS;product=hypothetical protein;protein_id=YP_006252305.1;transl_table=11
Streptococcus pneumoniae TIGR4 genus 78 hypothetical protein ID=cds29;Name=NP_344583.1;Parent=gene38;Dbxref=Genbank:NP_344583.1,GeneID:929780;gbkey=CDS;product=hypothetical protein;protein_id=NP_344583.1;transl_table=11
Streptococcus mitis B6 genus 35 Translation elongation factor TU ID=cds854;Name=YP_003446034.1;Parent=gene929;Dbxref=Genbank:YP_003446034.1,GeneID:8797981;gbkey=CDS;product=Translation elongation factor TU;protein_id=YP_003446034.1;transl_table=11
Streptococcus pneumoniae 670-6B genus 35 translation elongation factor Tu ID=cds793;Name=YP_003878976.1;Parent=gene805;Dbxref=Genbank:YP_003878976.1,GeneID:9729530;gbkey=CDS;product=translation elongation factor Tu;protein_id=YP_003878976.1;transl_table=11
Streptococcus pneumoniae 70585 genus 35 elongation factor Tu ID=cds1437;Name=YP_002740757.1;Parent=gene1488;Note=EF-Tu%3B promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis%3B when the tRNA anticodon matches the mRNA codon%2C GTP hydrolysis results%3B the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts%3B many prokaryotes have two copies of the gene encoding EF-Tu;Dbxref=Genbank:YP_002740757.1,GeneID:7684439;gbkey=CDS;product=elongation factor Tu;protein_id=YP_002740757.1;transl_table=11
Streptococcus pneumoniae A026 genus 35 elongation factor Tu ID=cds1209;Name=YP_008730608.1;Parent=gene1336;Note=EF-Tu%3B promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis%3B when the tRNA anticodon matches the mRNA codon%2C GTP hydrolysis results%3B the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts%3B many prokaryotes have two copies of the gene encoding EF-Tu;Dbxref=Genbank:YP_008730608.1,GeneID:17439784;gbkey=CDS;gene=tuf;product=elongation factor Tu;protein_id=YP_008730608.1;transl_table=11
Streptococcus pneumoniae ATCC 700669 genus 35 elongation factor Tu ID=cds1258;Name=YP_002511360.1;Parent=gene1394;Note=EF-Tu%3B promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis%3B when the tRNA anticodon matches the mRNA codon%2C GTP hydrolysis results%3B the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts%3B many prokaryotes have two copies of the gene encoding EF-Tu;Dbxref=Genbank:YP_002511360.1,GeneID:7329336;gbkey=CDS;product=elongation factor Tu;protein_id=YP_002511360.1;transl_table=11
[...]
The columns, left to right, are:
Species: The species/strain name of the genome to which the matches occurred.Disc. level: The taxonomic rank at which the peptide that matched this genome was discriminative.Count: The number of hits/matches accrued by this annotated region (total across the entire sample). Note that these counts are not quantitative, because each discriminative peptide can produce multiple matches to several different annotated regions in several different reference genome sequences.Product: Annotation for the protein product of this annotated region.Features: The raw feature string for this annotated region.
As we can see in this output, there are several hits to regions in different S. pneumoniae genomes, to regions annotated with hypothetical protein and elongation factor Tu. This sheet provides information that can be useful to identify potential biomarkers or help understand what regions of the studied bacteria are discriminative, and at what taxonomic level.
Note
The Hits to annotated regions output can also be printed to STDOUT using
the --print-annotations command line option. However, this is not
recommended as it is very verbose.
Discriminative peptides¶
The names and sequences of all discriminative peptides along with the rank at
which they were discriminative can be output to a text file using the
--write-discriminative-peptides command line option.
Antibiotic resistance¶
Detected expressed antibiotic resistance peptides are summarized in a text file. The output can look like this:
----------------------------------------------------------------------
Results for 124 discriminative peptides in tcup_tutorial_sample.fasta.ar.blast8
Disc. Hits % Family
64 84 0.5114 blaCTX-M
45 45 0.2739 blaTEM
10 10 0.0609 aac(3)-II
5 5 0.0304 mph(A)
Here, we see that the sample likely contains four different families of antibiotic resistance mechanisms: blaCTX-M, blaTEM, aac(3)-II, and mph(A). The columns, from left to right, are:
Disc.: The number of peptides that were discriminative to this family, i.e. peptides that did not match any other family.Hits: The number of aligned regions to this family that the discriminative peptides produced. This number of sometimes higher than the number of discriminative peptides, as each discriminative peptide can sometimes match to several variants within a family, or sometimes even several positions in the same protein.%: The proportion of peptides in the sample that were discriminative to this family.Family: The antibotic resistance gene family matched by discriminative peptides.