getBlastResults: Gets BLAST Results

In GeorgeLy7/DEGSimilar: A streamlined pipeline to compare DEGs via BLAST.

Description

A function that gets the BLAST hits of the submitted fasta file in the submitted fasta dabatase file. Creates a fasta database out of the user-submitted fastaDatabse file.

Usage

getBlastResults(
  userFasta,
  fastaDatabase,
  maxSequencesReturned = 5,
  dbType,
  userFastaType
)

Arguments

userFasta	A fasta file containing one fasta entry. This sequence is the one the users wishes to compare to the entries in the fastaDatabse file.
fastaDatabase	A fasta file containing fasta entries with sequences the user wishes to create a database out of and compare userFasta to.
maxSequencesReturned	The maximum amount of sequences that should be returned from the BLAST. Requires >= 1.
dbType	The sequence type of the database fasta. Is required to be "nucl" for nucleotide or "prot" for protein
userFastaType	The sequence type of the fasta to perorm BLAST on. Is required to be "nucl" for nucleotide or "prot" for protein

Value

Returns a list containing the BLAST result template.

• QueryID - The name of the query sequence

• SubjectID - The name of the matched sequence

• Perc.Ident - The percent identity of the sequence match

• Alignment.Length - The length of the alignment in the match

• Mismatches - The number of mismatches in the alignments

• Gap.Openings - The number of gaps in the alignment

• Q.start - The start of the alignment on the query sequence

• Q.end - The end of the alignment of the query sequence

• S.start - The start of the alignment on the subject sequence

• S.end - The end of the alignment of the subject sequence

• E - The E-value of the alignment

• Bits - The bit score of the alignment

Examples

# Example 1:
# Using the provided fasta query and database files
# data(databaseFasta)
# data(queryFasta)
# sink("tmpDatabase.fasta")
# cat(databaseFasta)
# sink("tmpQuery.fasta")
# cat(queryFata)
# blastResults <- getBlastResults("tmpQuery.fasta", "tmpDatabase.fasta", maxSequencesReturned=5, dbType="nucl", userFastaType="prot")
# blastResults

GeorgeLy7/DEGSimilar documentation built on Dec. 31, 2020, 12:04 p.m.