uniprotToFasta: Produces a fasta file that contains the desired Uniprot IDs'...

In helen307/phyMSAViewer: Provide Phylogenetic tree and MSA visualization from Uniprot IDs

Description

A function that produces a fasta file based on the Uniprot ID entered by the users.

Usage

uniprotToFasta(ID)

Arguments

ID	A character string that includes the Uniprot IDs separated by "OR"

Value

Creates a fasta file called seqs.fasta in the main directory.

References

1. Brennan, P. (1970, January 01). Drawing a simple phylogenetic tree of the human rel homology domain family. Retrieved December 04, 2020, from http://rforbiochemists.blogspot.com/2016/12/drawing-simple-phylogenetic-tree-of.html

2. Code for retrieving Uniprot data were borrowed from: http://rforbiochemists.blogspot.com/2016/12/drawing-simple-phylogenetic-tree-of.html

3. Pages, H., Aboyoun, P., Gentleman, R., & DebRoy, S. (2016). Biostrings: String objects representing biological sequences, and matching algorithms. R package version, 2(0), 10-18129.

4. Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290.

5. Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1), 28-36.

6. Charif, D., Lobry, J. R., Necsulea, A., Palmeira, L., Penel, S., Perriere, G., & Penel, M. S. (2020). Package ‘seqinr’.

Examples

# Use the following UniprotID for this function: P19838, Q00653, Q01201
## Not run: 
uniprotToFasta("AC=P19838 OR AC=Q00653 OR AC=Q01201")

## End(Not run)

# A file called seqs.fasta will appear in the main directory.

helen307/phyMSAViewer documentation built on Jan. 1, 2021, 3:16 a.m.