- Input sequences (in FASTA format)
Users can upload a sequence file or paste the sequence(s) in the submission page. All sequences must be in the FASTA format. To ensure that every sequence has a unique ID, we will check and assign an ID number to each sequence. Special characters (including white space, dot and comma) will be removed from the sequences. However, if a sequence contains illegal letters (e.g., numbers), the job will be terminated.
- Input GFF file (optional)
As an option, users can also provide gene information in GFF (General Feature Format) format. Otherwise, myRT will call FragGeneScan to predict protein coding genes. In the GFF file, the information of contig/genome ID, gene location and gene translation direction must be provided.
Output
- Visual summary shows the genomic neighborhood of Reverse Transcriptases in the reference genome, including the reverse transcriptase and a maximum of two genes on each side (intergenic regions less than 2000bp). Each RT is colored based on its predicted class RVT-DGR , RVT-CRISPR , RVT-GII (Group II introns), RVT-Retrons, RVT-Abi. Relevant domains that are fused to the RT genes and/or are in the flanking genes of the RTs are also color coded (e.g. cas1, cas2 , Avd, FGE_Sulfatase, YfmG , GIIM, RVT_N, HNHc.)
- Text files for download: gff file with all the annotated features (RT, genomic neighborhood), reverse transcriptases,genomic neighborhood and domains fused to RT, and so on.
- Zip folder for download: One Zip folder including all the results (See a sample File Descriptions here)
- For more information about DGR systems, checkout myDGR
- For more information about CRISPR-Cas systems, checkout CRISPRone
- Check out Demonstration examples
RT classes
- AbiA RTs are associated with Abortive Infection Systems (AbiA type)
- AbiK RTs are associated with Abortive Infection Systems (AbiK type)
- AbiP2 RTs are associated with Abortive Infection Systems in Phages
- CRISPR RTs are associated with CRISPR-Cas systems
- CRISPR-like RTs are similar to CRISPR RTs but lack the Cas1 or Cas2 domains that are fused to CRISPR RTs
- DGR RTs are associated with diversity generating retroelements
- Retron RTs are associated with Retron systems
- GII RTs are associated with Group II Intron systems
- G2L RTs are similar to GII RTs phylogenetically (G2L4, G2L, G2Lb, and G2Lc. G2L1 and G2L2 are called CRISPR RTs, and G2L3 RTs are called UG17 RT)
- UG RTs (UG1-UG28) RTs are groups of RTs without known functions (some may associate with defense systems in phage)
