A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

doi:10.1186/1471-2164-8-133

BMC Genomics

Volume 8

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Research article

A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

Sean Thomas¹ , LL Isadora Trejo Martinez² , Scott J Westenberger² and Nancy R Sturm²

¹Molecular Biology Institute, UCLA, Los Angeles, CA, USA

²Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, USA

author email corresponding author email

BMC Genomics 2007, 8:133doi:10.1186/1471-2164-8-133


Published:	24 May 2007

Additional files

Additional File 1:

Predicted fully edited mRNAs for CL Brener strain of T. cruzi (FASTA format). Sequences were generated by manually inserting or deleting Us in the unedited message sequence following the known sequences of the corresponding T. brucei edited mRNAs, while preserving conservation of the resulting amino acid sequence.

Format: FAS Size: 8KB Download file

Additional File 2:

Text file of predicted gRNAs. File contains predicted mRNA/gRNA hybridizations and scores for those predicted interactions. gRNAs were predicted from minicircle sequences using Smith-Waterman local alignments with predicted mRNA sequences listed in Additional File 1.

Format: TXT Size: 23KB Download file

Additional File 3:

PDF file containing maps of edited mRNA sequences showing sites of predicted gRNA associations, also indicated are the various DTUs of the strain from which the sequence is derived. The format of presentation is similar to that of Figure 4, 5, 6, with the gRNA sequences shown below the predicted mRNA sequences.

Format: PDF Size: 116KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional File 4:

Image (png format) of HMM test to predict gRNAs obtained by local alignment (LA). Presented in pairs of lines, this spectrogram alignment represent gRNA predictions with the first line representing the HMM prediction and the second line in each pair representing the LA prediction. Line 1 and line 2 therefore represent the HMM and LA gRNA predictions (respectively) for the same sequence, and lines 3 and 4 the HMM and LA predictions for a separate minicircle sequence. A pair of lines is presented for each gRNA sequence with overlapping predictions.

Format: PNG Size: 435KB Download file

Additional File 5:

This file lists the most likely gRNA sequence from each T. cruzi minicircle sequence as predicted using the HMM. FASTA format. An 85% accuracy is expected for those variable regions that do contain gRNAs. The fraction of variable regions that do not contain a functioning gRNA is not known, and for this reason some of these sequences may represent false predictions.

Format: FAS Size: 15KB Download file