ATRHUNTER

[…] statistically significant pairwise similarity, these approaches are unable to find the latent periodicity. first of all, it involves algorithms and programs, such as trf [], mreps [], trstalker [], atrhunter [], t-reks [], imex [, ], crisprs [], swan [], and some others [, ], because similarity between the different periods is very low in case of latent periodicity. this leads to the lack […]

[…] with the best performing algorithm reducing the error rate by 37% compared to the baseline. it would be interesting to explore other programs for detecting tandem repeats, such as mreps [] or atrhunter []., in addition to the baseline three-state model, we have compared our approach to other alignment programs context [] and muscle []. the context program, which uses context-sensitive […]

[…] exact-repeat motifs) using the “ssr” computer program [,], and for non-perfect ssr (np-ssr, i.e. non-exact repeat motifs) using the “atr hunter” computer program ( http://bioinfo.cs.technion.ac.il/atrhunter/atrhunter.htm[]). perfect ssr included mononucleotide repeats (mnr) with longer than 5-bp repeats, and large ssr with motif size ≥3 bp repeated more than twice. np-ssr included only ssr […]

[…] algorithms for finding trs, even when mutations occur with non-negligible probability. tandem repeat finder (trf) [], crisprfinder [], mreps [], reputer [], approximate tandem repeat hunter (atrhunter) [], tandemswan [], and tread [] are some examples of currently operational systems that can be accessed via a web interface., comparative studies [,], for the case of short trs with high […]