Package 'MINTplates'

Title: Encode "License-Plates" from Sequences and Decode Them Back
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>.
Authors: Shanliang Zhong [aut, cre]
Maintainer: Shanliang Zhong <[email protected]>
License: GPL (>= 2)
Version: 1.0.1
Built: 2024-12-01 08:42:42 UTC
Source: CRAN

Help Index

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)