Package 'CleanBSequences'

Title: Curing of Biological Sequences
Description: Curates biological sequences massively, quickly, without errors and without internet connection. Biological sequences curing is performed by aligning the forward and / or revers primers or ends of cloning vectors with the sequences to be cleaned. After the alignment, new subsequences are generated without biological fragment not desired by the user. Pozzi et al (2020) <doi:10.1007/s00438-020-01671-z>.
Authors: Florencia I. Pozzi, Silvina A. Felitti
Maintainer: Florencia I. Pozzi <[email protected]>
License: GPL (>= 2)
Version: 2.3.0
Built: 2024-12-06 06:35:11 UTC
Source: CRAN

Help Index

Curing of biological sequences

Description

Curates biological sequences of primer reverse.This cleaning is required for techniques such as cDNA-AFLP.

Usage

DNAStringSetOPR(SEQs, PrimerR)

Arguments

SEQs

file with fasta format containing biological sequences that are to be cleaned.
PrimerR

dnastring containing the reverse primer/vector sequences to be removed.

Value

clean biological sequences and visualization of the alignments

Author(s)

Florencia I Pozzi, Silvina A. Felitti

Examples

SEQs = readDNAStringSet(system.file("sequences","SeqInputOPR.fasta", package = "CleanBSequences"))
PrimerR= DNAString ("GACTGCGTACCATGC")
DNAStringSetOPR (SEQs,PrimerR)

Curing of biological sequences

Description

Curates biological sequences of two restriction enzyme primers or cloning vectors.This cleaning is required for techniques such as cDNA-AFLP.This cleaning is required for techniques such as cDNA-AFLP.

Usage

DNAStringSetTPR(SEQs, PrimerF, PrimerR)

Arguments

SEQs

file with fasta format containing biological sequences that are to be cleaned.
PrimerF

dnastring containing the foward primer/vector sequences to be removed.
PrimerR

dnastring containing the reverse primer/vector sequences to be removed.

Value

clean biological sequences and visualization of the alignments

Author(s)

Florencia I Pozzi, Silvina A. Felitti

Examples

SEQs = readDNAStringSet(system.file("sequences","SeqInputTPR.fasta", package = "CleanBSequences"))
PrimerR= DNAString ("GACTGCGTACCATGC")
PrimerF = DNAString("GATGAGTCCTGACCGAA")
DNAStringSetTPR (SEQs,PrimerF,PrimerR)

Clean biological secuences

Description

Curates biological sequences of primer reverse.This cleaning is required for techniques such as cDNA-AFLP.

Usage

OnePrimerRemove(SEQs, PrimerR)

Arguments

SEQs

dnastring containing biological sequences that are to be cleaned.
PrimerR

dnastring containing the reverse primer/vector sequences to be removed.

Value

clean biological sequences and visualization of the alignments

Author(s)

Florencia I Pozzi and Silvina A. Felitti

Examples

SEQs = DNAString(paste("GCCTCGCCTCCCTCTTTGATCAGCTTCGCATATCAGGCAACAGCTCAATTT",
"GGTACTTGTTCAAATAAGCATTTAGACCATCTGTTCCAAGAACCTTTGCAATCTT",
"CACAAGGTGGTCATGGTACGCAGTC", sep=""))
PrimerR= DNAString("GACTGCGTACCATGC")
OnePrimerRemove (SEQs,PrimerR)

Clean biological secuences

Description

Curates biological sequences of two restriction enzyme primers or cloning vectors.This cleaning is required for techniques such as cDNA-AFLP.

Usage

TwoPrimerRemove(SEQs, PrimerF, PrimerR)

Arguments

SEQs

DNAString containing biological sequences that are to be cleaned.
PrimerF

dnastring containing the foward primer/vector sequences to be removed.
PrimerR

dnastring containing the reverse primer/vector sequences to be removed.

Value

clean biological sequences and visualization of the alignments

Author(s)

Florencia I Pozzi, Silvina A. Felitti

Examples

SEQs = DNAString(paste("ACTTTCTGCTGCTTGTGGTCGCAATCAGAGTCCTGATGATGAGTCCTGA",
"CCGAACCCTTTTTCTCCGTCATCCGTTGGTCCATGGTACGCAATCAGAG", sep = ""))
PrimerF = DNAString("GATGAGTCCTGACCGAA")
PrimerR = DNAString("GACTGCGTACCATGC")
TwoPrimerRemove (SEQs,PrimerF,PrimerR)