| Type: | Package |
| Title: | Curing of Biological Sequences |
| Version: | 2.3.0 |
| Author: | Florencia I. Pozzi, Silvina A. Felitti |
| Maintainer: | Florencia I. Pozzi <florenciapoz@hotmail.com> |
| 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>. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| Depends: | pwalign, Biostrings |
| RoxygenNote: | 7.3.1 |
| NeedsCompilation: | no |
| Packaged: | 2024-05-09 04:01:00 UTC; ADMIN |
| Repository: | CRAN |
| Date/Publication: | 2024-05-09 18:10:02 UTC |
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)