This function reads a file storing a specific sequence type, such as "cds", "protein", or
"dna" in a standard sequence file format such as "fasta", etc. and depending of the makedb
parameter either creates a blast-able database, or returns the corresponding protein sequences
as data.table object for further BLAST searches.
set_blast(
file,
seq_type = "cds",
format = "fasta",
makedb = FALSE,
delete_corrupt_cds = TRUE,
path = NULL,
makedb_type = "protein",
...
)a character string specifying the path to the file storing the sequences of interest.
a character string specifying the sequence type stored in the input file.
Options are are: "cds", "protein", or "dna". In case of "cds", sequence are translated to protein sequences,
in case of "dna", cds prediction is performed on the corresponding sequences which subsequently are
translated to protein sequences. Default is seq_type = "cds".
a character string specifying the file format used to store the genome, e.g. "fasta", "gbk".
TRUE or FALSE whether a database should be created or not (BLAST parameter 'makeblastdb').
a logical value indicating whether sequences with corrupt base triplets should be removed from the input file. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.
a character string specifying the path to the BLAST program (in case you don't use the default path).
a character string specifying the sequence type stored in the BLAST database
that is generated using 'makeblastdb'. Options are: "protein" and "nucleotide". Default is makedb_type = "protein".
additional arguments that are used by the seqinr::read.fasta() function.
A list storing two elements. The first element [[1]] corresponds to the data.table storing the gene ids in the first column and the corresponding dna (cds) sequence in the second column and the aminoacid sequence third column. The second list element [[2]] stores the name of the protein database that was created by 'makeblastdb'.
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.
Gish, W. & States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.
Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.
Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.
Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.
Zhang, J. & Madden, T.L. (1997) "PowerBLAST: A new network BLAST application for interactive or automated sequence analysis and annotation." Genome Res. 7:649-656.
Morgulis A., Coulouris G., Raytselis Y., Madden T.L., Agarwala R., & Schaeffer A.A. (2008) "Database indexing for production MegaBLAST searches." Bioinformatics 15:1757-1764.
Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., & Madden T.L. (2008) "BLAST+: architecture and applications." BMC Bioinformatics 10:421.
if (FALSE) {
# running the set function to see an example output
head(set_blast(file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'))[[1]] , 2)
}