The typical data retrieving of tRFtarget includes 3 ways:
For each data retrieving way of tRFtarget, an additional filter of free energy and maximum complementary length can be used to filter out less likely interactions with higher free energy and shorter maximum complementary length.
The retrieved data from tRFtarget will be formatted into a tabular form for display, and the result table supports following operations:
We provide several buttons to perform downstream analysis conveniently.
tRFtarget will report the maximum complementary length (MCL) feature of a specific binding site on a transcript. The MCL is defined as the length of the longest successively complementary sequences. For example, the figure below shows a binding interaction between tRF tRF-5013b and transcript ARF-201 predicted by RNAhybrid. The interaction has 3 distinct parts of complementary sequences as covered by green lines. The lengths of complementary sequences of the 3 parts are 6, 5, and 7, respectively. Therefore, the MCL of this interaction is 7 bases.
IntaRNA tool will return similar binding interactions between the same tRF and transcript, and among these similar entries only the one with the lowest free energy will be kept. For example, all the 5 binding interactions between tRF tRF-3001a and transcript DCTPP1-201 predicted by IntaRNA are shown in the below figure. The 5 interactions have the similar interaction structure, and are almost in the identical location on the transcript. So only the toppest one entry with the lowest free energy (-20.36 kcal/mol) is kept and stored in tRFtarget database, while the other 4 entries will be defined as duplicated entries and discarded.
1 RNAhybrid prediction and 1 IntaRNA predction will be defined as consensus if them have a similar interaction structure. The interaction need to be on the identical location on the transcrpt, allowing a 2 bases offset on the beginning and/or ending of the interaction sequence. For example, the RNAhybrid prediction and IntaRNA predction of tRF-1001 and trandcript ARF1-213 are defined as consensus (see figure below). The beginning site of both predictions are identical, while the ending site has a offset of 1 base (RNAhybrid prediction ends on the 1683rd base while IntaRNA predction ends on the 1682nd base).