Tandem Repeat analysis for TRAL class 2, 3 and 24. (Back to main download page)
It is possible that some CL-EXTs were missed by MAAB due to a strict criterion for an ER signal sequence, thereby excluding some partial sequences. To address this we generated a tandem repeat annotation library (TRAL) (Schaper et al., 2015). The TRAL library identified all repeats in class 2 (CL-EXTs) sequences that were longer than 10 amino acids, present in ≥4 copies and significantly different from random sequence evolution (p-value < 0.05). Libraries were also generated for MAAB class 3 (PRP) and class 24 (<15% known motifs) sequences. Each repeat was used to construct a circular sequence profile hidden Markov model and these models were used to search the MAAB input (1KP multiple assembly data) to identify all sequences that contain these repeats. A simple tool for browsing the results of TRAL is provided below, using MSAViewer to display alignments.