| Title: | Encode "License-Plates" from Sequences and Decode Them Back |
| Version: | 1.0.1 |
| Description: | It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>. |
| Depends: | R (≥ 3.2.3) |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| RoxygenNote: | 7.1.1 |
| URL: | http://www.bio-inf.cn/ |
| NeedsCompilation: | no |
| Packaged: | 2021-09-02 23:38:03 UTC; admin |
| Author: | Shanliang Zhong [aut, cre] |
| Maintainer: | Shanliang Zhong <slzhong@foxmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2021-09-03 06:50:07 UTC |
Annotate a tRF sequence
Description
Obtain tRF ID, type, whether exclusive to tRNA space, and tRNA sources of the tRF with its sequence.
Usage
annotate_tRF(sequence)
Arguments
sequence |
tRF sequence. |
Value
tRF ID, type, whether exclusive to tRNA space, and tRNA sources of the tRF.
References
Loher P, Telonis AG, Rigoutsos I. Sci Rep (2017) <doi: 10.1038/srep41184>
Examples
sequence='TCCCTGGTGGTCTAGTGGTTAGGATTCGGC'
annotate_tRF(sequence)
Decode license-plates
Description
Decode the license-plates using the lookup table.
Usage
deseqs(plates)
Arguments
plates |
The license plates being decoded. |
Value
The sequences they decodes to.
References
Pliatsika V, Loher P, Telonis AG, Rigoutsos I. Bioinformatics (2016) <doi: 10.1093/bioinformatics/btw194>
Examples
plates=c('tRF-18-BS6PDFD2','tRF-20-51K36D26')
deseqs(plates)
Encode sequences
Description
Encode the sequences into their corresponding license plates with given prefix (if given one).
Usage
enseqs(sequences, prefix = "")
Arguments
sequences |
The sequences being encoded. |
prefix |
The prefix to use for the license plate. |
Value
The license plates they encode to.
References
Pliatsika V, Loher P, Telonis AG, Rigoutsos I. Bioinformatics (2016) <doi: 10.1093/bioinformatics/btw194>
Examples
seqs=c('AACCGGGCAGAAGCACCA','GAGCCCCAGTGGAACCACCA')
enseqs(seqs,'tRF')
Determine whether the tRFs are exclusive to tRNA space
Description
Determine whether the tRFs are exclusive to tRNA space with the tRF sequences.
Usage
exclusive(sequences)
Arguments
sequences |
tRF sequences. |
Value
Whether the tRFs are exclusive to tRNA space.
References
Loher P, Telonis AG, Rigoutsos I. Sci Rep (2017) <doi: 10.1038/srep41184>
Examples
sequences=c('TCCCTGGTGGTCTAGTGGTTAGGATTCGGC','TCCCTGGTGGTCTAGTGGTTAGGATTCGGCG')
exclusive(sequences)
Obtain the tRNA source of a tRF
Description
Obtain the tRNA source of a tRF with the tRF sequence.
Usage
source_tRNA(sequence)
Arguments
sequence |
tRF sequence. |
Value
Sources of the tRF.
References
Loher P, Telonis AG, Rigoutsos I. Sci Rep (2017) <doi: 10.1038/srep41184>
Examples
sequence='TCCCTGGTGGTCTAGTGGTTAGGATTCGGC'
source_tRNA(sequence)
Obtain the tRNA sources of tRFs
Description
Obtain the tRNA sources of tRFs with the tRF sequences.
Usage
source_tRNA2(sequences)
Arguments
sequences |
tRF sequences. |
Value
Sources of the tRFs.
References
Loher P, Telonis AG, Rigoutsos I. Sci Rep (2017) <doi: 10.1038/srep41184>
Examples
sequences=c('TCCCTGGTGGTCTAGTGGTTAGGATTCGGC','TCCCTGGTGGTCTAGTGGCT','TCCCTGGTGGTCTAATGGTTA')
source_tRNA2(sequences)
Obtain the type of tRFs
Description
Obtain the type of tRFs with the tRF sequences.
Usage
tRFtype(sequences)
Arguments
sequences |
tRF sequences. |
Value
The type of tRFs.
References
Loher P, Telonis AG, Rigoutsos I. Sci Rep (2017) <doi: 10.1038/srep41184>
Examples
sequences=c('TCCCTGGTGGTCTAGTGGTTAGGATTCGGC','AAAAATTTTGGTGCAACTCCAAATAAAA')
tRFtype(sequences)