Spreadsheet: 969b22a9-4f0c-4360-9521-c38a5b96149a
Sheet: Sheet1

Designation | Id assigned to peptide sequence
Sequence | Sequence of the peptide
Predicted PEP77.2 [NAME]? | Alignment of gene or read containing the peptide shows that the peptide aligns with the same region as the published H-2Kb epitopes pep77.2, [NAME] and PA14 (alignment performed by ClustalW [1]).
Original Source | Source of the sequence in which the peptide was originally found (published sequences from GenBank or TSC (T. cruzi Sequencing Consortium) raw sequence reads)
Present in TSC Genome? | If the peptide is present in the TSC T cruzi genome, then the sequence type with highest precedence is shown. The precedence hierararchy is: 1) CL Brener Strain annotated ts gene, 2) CL Brener Strain annotated ts pseudogene, 3) CL Brener strain ts reads, 4) [NAME] strain ts ORFs, 5) [NAME] strain ts reads. If the peptide was not found in any TSC genome sequences, then "Not found" is shown.
IFNg ELISPOT (+tests/total) | Number of mice in which peptide-induced IFNg spot forming units were increased 2-fold over unstimulated cells, over the total number of mice tested for that peptide, n.d. = not done.
In vivo CTL | In vivo killing of peptide loaded target cells.  (+) if the peptide loaded target cells are killed in greater than 50% of mice tested, (-) if they are not, n.d. = not done.
RMA-S MHC-binding assay | Relative MHC I binding based on peptide-induced stabilization of H-2kb on RMA-S cells.  (++) if the median fluorescence intensity (MFI) of anti-H-2Kb staining following peptide incubation is within 75% of the TSKB20 (the strongest binder)-induced stabilization.  (+) if the MFI of anti-H-2Kb staining is 25-75% of TSKB20-induced stabilization but more than 2-fold higher than non-peptide loaded RMA-S cells.  (-) if the MFI of the anti-H-2Kb staining is less than twice the level of non-peptide-pulsed cells, n.d. = not done.
[NAME]? | Yes if the peptide sequence matches the H-2Kb sequence motif: XXXX[F,Y]XX[A,I,L,T,V,M]
Predicted Kb Binding Affinity (PIC50) | Sequence-based, computationally derived disassociation constant value for the peptide w/ H-2Kb MHC (smaller value indicates higher binding affinity, maximum of 500nM [2])
Predicted Kb Binding Free Energy Score | Structure-based, computationally derived free energy score for the peptide w/ H-2Kb MHC (smaller value indicates tighter conformation, prediction by PREDEP [3]).
Relative Frequency CL Brener/Esmeraldo Raw Sequence Reads | Comparison of the frequency of the peptide in the CL Brener and [NAME] raw sequence reads. If the peptide was found in both the CL Brener and the [NAME] raw sequence reads (see columns: "# Occurrences in TSC CL Brener Raw Sequence Reads (3 Frames)" and "# Occurrences in TSC Esmeraldo Raw Sequence Reads (3 Frames)") then the value shown was derived by dividing the peptide frequency in the database with the higher frequency by the peptide frequency in the database with the lower frequency (if the frequency in Esmeraldo strain is higher than CL Brener strain, this value is also negated to aid differentiating relative frequencies when sorting). Otherwise, the database that contains the peptide is shown ("Not present in either" if present in neither set of sequence reads).
Relative Frequency CL Brener/[NAME] trans-sialidase Genes/ORFs | Similar analysis as performed for "Relative Frequency CL Brener/Esmeraldo Raw Sequence Reads" except that the frequency of CL Brener ts genes and [NAME] ts ORFs was used. For a description of how the [NAME] ORFs were obtained, see the "Materials and Methods" section of the manuscript.
# Occurrences in TSC CL Brener Raw Sequence Reads (3 Frames) | The number of occurrences of the peptide in the 1,131,562 raw sequence reads in the TSC CL Brener strain T cruzi genome. The occurrences were determined by using TBLASTN of the peptides (amino acid sequence) against the reads (DNA sequences) and counting the exact matches in any reading frame.
Frequency of Peptide in CL Brener Reads (per 10000 reads) | Frequency of the peptide in the TSC CL Brener raw sequence reads, obtained by dividing the value in "# Occurrences in TSC CL Brener Raw Sequence Reads (3 Frames)" by 1,131,562 (total number of reads) and multiplying by 10,0000.
# Occurrences in TSC CL Brener Annotated trans-sialidase Genes | The number of occurrences of the peptide in the 735 annotated trans-sialidase genes (no pseudogenes) in the TSC CL Brener strain T cruzi genome. The occurrences were determined by using BLASTP of the peptides (amino acid sequence) against the genes (amino acid sequence) and counting the exact matches.
Frequency of Peptide in CL Brener Annotated trans-sialidase Genes (percentage) | Frequency of the peptide in the TSC CL Brener  trans-sialidase genes, obtained by dividing the value in "# Occurrences in TSC CL Brener Annotated trans-sialidase Genes" by 735 (total number of annotated ts genes) and multiplying by 100.
# Occurrences in TSC CL Brener trans-sialidase Pseudogenes (3 Frames) | The number of occurrences of the peptide in the 695 annotated trans-sialidase pseudogenes in the TSC CL Brener strain T cruzi genome. The occurrences were determined by using TBLASTN of the peptides (amino acid sequence) against the pseudogenes (DNA sequences) and counting the exact matches.
# Occurrences in TSC Esmeraldo Raw Sequence Reads (3 Frames) | The number of occurrences of the peptide in the 154,155 raw sequence reads in the TSC Esmeraldo strain T cruzi genome. The occurrences were determined by using TBLASTN of the peptides (amino acid sequence) against the reads (DNA sequences) and counting the exact matches in any reading frame.
Frequency of Peptide in Esmeraldo Reads (per 10000 reads) | Frequency of the peptide in the TSC Esmeraldo raw sequence reads, obtained by dividing the value in "# Occurrences in TSC Esmeraldo Raw Sequence Reads (3 Frames)" by 154,155 (total number of reads) and multiplying by 10,0000.
# Occurrences in TSC Esmeraldo trans-sialidase ORFs | The number of occurrences of the peptide in 565 ORFs with homology to annotated CL Brener strain trans-sialidase genes in the TSC Esmeraldo strain T cruzi genome. The occurrences were determined by using BLASTP of the peptides (amino acid sequence) against the ORFs (amino acid sequence) and counting the exact matches.
Frequency of Peptide [NAME] trans-sialidase ORFs (percentage) | Frequency of the peptide in the TSC Esmeraldo strain trans-sialidase ORFs, obtained by dividing the value in "# Occurrences in TSC Esmeraldo trans-sialidase ORFs" by 565 (total number of trans-sialidase ORFs) and multiplying by 100.
# CL Brener trans-sialidase Genes w/ Predicted GPI Anchor | The number of trans-sialidase genes in the TSC CL Brener strain T cruzi genome containing the peptide that are predicted to contain a GPI anchor (using DGPI [4]).
# CL Brener trans-sialidase Genes w/ Predicted Signal Peptide | The number of trans-sialidase genes in the TSC CL Brener strain T cruzi genome containing the peptide that are predicted to contain a signal peptide (using SignalP 2.0 [5] hidden [NAME] model).
# Occurrences in TSC CL Brener Whole Proteome | The number of genes in the TSC CL Brener strain T cruzi genome containing the peptide that were identified in the T cruzi proteome  [6].
# Occurrences in TSC CL Brener Amastigote Proteome | The number of genes in the TSC CL Brener strain T cruzi genome containing the peptide that were identified with high-confidence in the amastigote life-cycle stage in the T cruzi proteome.
# Occurrences in TSC CL Brener Trypomastigote Proteome | The number of genes in the TSC CL Brener strain T cruzi genome containing the peptide that were identified with high-confidence in the trypomastigote life-cycle stage in the T cruzi proteome.
# Occurrences in TSC CL Brener Metacyclic Proteome | The number of genes in the TSC CL Brener strain T cruzi genome containing the peptide that were identified with high-confidence in the metacyclic life-cycle stage in the T cruzi proteome.
# Occurrences in TSC CL Brener Epimastigote Proteome | The number of genes in the TSC CL Brener strain T cruzi genome containing the peptide that were identified with high-confidence in the epimastigote life-cycle stage in the T cruzi proteome.
REFERENCES
1.  Chenna, R., [NAME], T. Koike, [NAME], [NAME], [NAME], and [NAME]. 2003. Multiple sequence alignment with the Clustal series of
2.  Gulukota, K., [NAME], [NAME], and [NAME]. 1997. Two complementary methods for predicting peptides binding major histocompatibility complex
3. Altuvia, [NAME] and [NAME]. 2004. A structure-based approach for prediction of MHC-binding peptides. Methods 34:454-9.
4. [NAME], J. and D. Buloz, (1999), "Detection/prediction of GPI cleavage site (GPI-anchor) in a protein (DGPI)", Retrieved [retrieve date] from http://129.194.185.165/dgpi/
5. [NAME], H., and [NAME].  Prediction of signal peptides and signal anchors by a hidden [NAME] model.1998.  In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB 6 ), AAAI Press, Menlo Park, California, pp. 122—130.
6.  [NAME], J. A., 3rd, [NAME], [NAME], [NAME], [NAME], [NAME]