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https://doi.org/10.21256/zhaw-3884| Publication type: | Article in scientific journal |
| Type of review: | Peer review (publication) |
| Title: | TRAL : tandem repeat annotation library |
| Authors: | Schaper, Elke Korsunsky, Alexander Pečerska, Jūlija Messina, Antonio Murri, Riccardo Stockinger, Heinz Zoller, Stefan Xenarios, Ioannis Anisimova, Maria |
| DOI: | 10.21256/zhaw-3884 10.1093/bioinformatics/btv306 |
| Published in: | Bioinformatics |
| Volume(Issue): | 31 |
| Issue: | 18 |
| Page(s): | 3051 |
| Pages to: | 3053 |
| Issue Date: | 2015 |
| Publisher / Ed. Institution: | Oxford University Press |
| ISSN: | 1367-4803 1367-4811 |
| Language: | English |
| Subjects: | Molecular sequence; Profile hidden Markov models; Tandem repeat; Bioinformatics |
| Subject (DDC): | 004: Computer science 572: Biochemistry |
| Abstract: | Motivation: Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results. Results: We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly. |
| Further description: | Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch) |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/8265 |
| Fulltext version: | Published version |
| License (according to publishing contract): | Licence according to publishing contract |
| Restricted until: | 2019-01-01 |
| Departement: | Life Sciences and Facility Management |
| Organisational Unit: | Institute of Computational Life Sciences (ICLS) |
| Appears in collections: | Publikationen Life Sciences und Facility Management |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| btv306.pdf | 172.66 kB | Adobe PDF |  View/Open |
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