tidysq contains tools for analysis and manipulation ofbiological sequences (including amino acid and nucleic acid – e.g. RNA,DNA – sequences). Two major features of this package are:
effective compression of sequence data, allowing to fit largerdatasets inR,
compatibility with most oftidyverse universe,especiallydplyr andvctrs packages, makinganalysestidier.
Tryour quick start vignette orour exhaustivedocumentation.
The easiest way to installtidysq package is to downloadits latest version from CRAN repository:
install.packages("tidysq")Alternatively, it is possible to download the development versiondirectly from GitHub repository:
# install.packages("devtools")devtools::install_github("BioGenies/tidysq")library(tidysq)file<-system.file("examples","example_aa.fasta",package ="tidysq")sqibble<-read_fasta(file)sqibble#> # A tibble: 421 × 2#> sq name#> <ami_bsc> <chr>#> 1 PGGGKVQIV <13> AMY1|K19|T-Protein (Tau)#> 2 NLKHQPGGG <43> AMY9|K19Gluc41|T-Protein (Tau)#> 3 NLKHQPGGG <19> AMY14|K19Gluc782|T-Protein (Tau)#> 4 GKVQIVYK <8> AMY17|PHF8|T-Protein (Tau)#> 5 VQIVYK <6> AMY18|PHF6|T-Protein (Tau)#> 6 DAEFRHDSG <40> AMY22|Whole|Amyloid beta A4 peptide#> 7 VPHQKLVFF <15> AMY23|HABP1|Amyloid beta A4 peptide#> 8 VHPQKLVFF <15> AMY24|HABP2|Amyloid beta A4 peptide#> 9 VHHPKLVFF <15> AMY25|HABP3|Amyloid beta A4 peptide#> 10 VHHQPLVFF <15> AMY26|HABP4|Amyloid beta A4 peptide#> # ℹ 411 more rowssq_ami<- sqibble$sqsq_ami#> basic amino acid sequences list:#> [1] PGGGKVQIVYKPV <13>#> [2] NLKHQPGGGKVQIVYKPVDLSKVTSKCGSLGNIHHKPGGGQVE <43>#> [3] NLKHQPGGGKVQIVYKEVD <19>#> [4] GKVQIVYK <8>#> [5] VQIVYK <6>#> [6] DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV <40>#> [7] VPHQKLVFFAEDVGS <15>#> [8] VHPQKLVFFAEDVGS <15>#> [9] VHHPKLVFFAEDVGS <15>#> [10] VHHQPLVFFAEDVGS <15>#> printed 10 out of 421# Subsequences can be extracted with bite()bite(sq_ami,5:10)#> Warning in CPP_bite(x, indices, NA_letter, on_warning): some sequences are#> subsetted with index bigger than length - NA introduced#> basic amino acid sequences list:#> [1] KVQIVY <6>#> [2] QPGGGK <6>#> [3] QPGGGK <6>#> [4] IVYK!! <6>#> [5] YK!!!! <6>#> [6] RHDSGY <6>#> [7] KLVFFA <6>#> [8] KLVFFA <6>#> [9] KLVFFA <6>#> [10] PLVFFA <6>#> printed 10 out of 421# There are also more traditional functionsreverse(sq_ami)#> basic amino acid sequences list:#> [1] VPKYVIQVKGGGP <13>#> [2] EVQGGGPKHHINGLSGCKSTVKSLDVPKYVIQVKGGGPQHKLN <43>#> [3] DVEKYVIQVKGGGPQHKLN <19>#> [4] KYVIQVKG <8>#> [5] KYVIQV <6>#> [6] VVGGVMLGIIAGKNSGVDEAFFVLKQHHVEYGSDHRFEAD <40>#> [7] SGVDEAFFVLKQHPV <15>#> [8] SGVDEAFFVLKQPHV <15>#> [9] SGVDEAFFVLKPHHV <15>#> [10] SGVDEAFFVLPQHHV <15>#> printed 10 out of 421# find_motifs() returns a whole tibble of useful informationsfind_motifs(sqibble,"^VHX")#> # A tibble: 9 × 5#> names found sought start end#> <chr> <ami_bsc> <chr> <int> <int>#> 1 AMY24|HABP2|Amyloid beta A4 peptide VHP <3> ^VHX 1 3#> 2 AMY25|HABP3|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 3 AMY26|HABP4|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 4 AMY34|HABP12|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 5 AMY35|HABP13|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 6 AMY36|HABP14|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 7 AMY38|HABP16|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 8 AMY43|AB5|Amyloid beta A4 peptide VHH <3> ^VHX 1 3#> 9 AMY195|86-95|Prion protein (human) VHD <3> ^VHX 1 3An example ofdplyr integration:
library(dplyr)# tidysq integrates well with dplyr verbssqibble%>%filter(sq%has%"VFF")%>%mutate(length =get_sq_lengths(sq))#> # A tibble: 24 × 3#> sq name length#> <ami_bsc> <chr> <dbl>#> 1 DAEFRHDSG <40> AMY22|Whole|Amyloid beta A4 peptide 40#> 2 VPHQKLVFF <15> AMY23|HABP1|Amyloid beta A4 peptide 15#> 3 VHPQKLVFF <15> AMY24|HABP2|Amyloid beta A4 peptide 15#> 4 VHHPKLVFF <15> AMY25|HABP3|Amyloid beta A4 peptide 15#> 5 VHHQPLVFF <15> AMY26|HABP4|Amyloid beta A4 peptide 15#> 6 KKLVFFPED <9> AMY32|HABP10|Amyloid beta A4 peptide 9#> 7 VHHQEKLVF <16> AMY34|HABP12|Amyloid beta A4 peptide 16#> 8 VHHQEKLVF <16> AMY35|HABP13|Amyloid beta A4 peptide 16#> 9 VHHQEKLVF <16> AMY36|HABP14|Amyloid beta A4 peptide 16#> 10 KKLVFFAED <9> AMY37|HABP15|Amyloid beta A4 peptide 9#> # ℹ 14 more rowsFor citation type:
citation("tidysq")or use:
Michal Burdukiewicz, Dominik Rafacz, Laura Bakala, Jadwiga Slowik,Weronika Puchala, Filip Pietluch, Katarzyna Sidorczuk, Stefan Roedigerand Leon Eyrich Jessen (2021). tidysq: Tidy Processing and Analysis ofBiological Sequences. R package version 1.1.3.