BLAST 2 Sequence strings

BLAST 2 nucleotide or protein strings with a QuickBLAST instance.

BLAST2Seqs(ptr, query, subject, verbose = TRUE)

Arguments

ptr

(Rcpp::XPtr<QuickBLAST>) or (unsigned int) Pointer/ID of QuickBLAST instance

query

(string) Query sequence

subject

(string) Subject sequence.

verbose

(bool) Verbosity (Default: TRUE).

Value

(Rcpp::XPtr<QuickBLAST>) Pointer to a QuickBLAST Instance (Cannot be used in R)

See also

GetInstanceID(), GetQuickBLASTInstance(), BLAST2Files(), BLAST2Seqs(), BLAST2Folders(), BLAST1Folder(), RemoteBLAST()

Examples

blastp_inst <- QuickBLAST::CreateQuickBLASTInstance(
  seq_type = 1,
  strand = 0,
  program = "blastp",
  save_sequences = FALSE,
  save_hsp_sequences = FALSE
)
#> Using blastp Defaults...
QuickBLAST::BLAST2Seqs(
  blastp_inst,
  "MQILLVEDDNTLFQELKKELEQWDFNV
  AGIEDFGKVMDTFESFNPEIVILDVQLP
  KYDGFYWCRKMREVSNVPILFLSSRDNP
  MDQVMSMELGADDYMQKPFYTNVLIAKL
  QAIYRRVYEFTAEEKRTLTWQDAVVDLS
  KDSIQKGDDTIFLSKTEMIILEILITKK
  NQIVSRDTIITALWDDEAFVSDNTLTVN
  VNRLRKKLSEISMDSAIETKVGKGYMAHE",
  "MQILLVEDDNTLFQELKKELEQWDFNV
  AGIEDFGKVMDTFESFNPEIVILDVQLP
  KYDGFYWCRKMREVSNVPILFLSSRDNP
  MDQVMSMELGADDYMQKPFYTNVLIAKL
  QAIYRRVYEFTAEEKRTLTWQDAVVDLS
  KDSIQKGDDTIFLSKTEMIILEILITKK
  NQIVSRDTIITALWDDEAFVSDNTLTVN
  VNRLRKKLSEISMDSAIETKVGKGYMAHE"
)
#> Clock : 0.00244417 seconds
#> 1
#> RecordBatchVector size: 1
#> Total rows across all batches: 1
#> [[1]]
#>   seq_info_num_alignments seq_info_seqids_qseqid seq_info_seqids_sseqid
#> 1                       1                      1                      2
#>   seq_info_seqs_qseq seq_info_seqs_sseq seq_info_strands seq_info_lengths_qlen
#> 1                                                    */*                   224
#>   seq_info_lengths_slen hsps_qhsp hsps_shsp hsps_pident hsps_pident_gap
#> 1                   224                             100             100
#>   hsps_frames   hsps_evalue hsps_length hsps_length01 hsps_qstart hsps_qend
#> 1         0/0 9.626626e-172         224             1           1       224
#>   hsps_sstart hsps_send hsps_bitscore hsps_score hsps_qcovhsp hsps_blast_score
#> 1           1       224      458.7585       1179            0             1179
#>   hsps_gaps hsps_nident hsps_mismatch hsps_positive hsps_n_splices hsps_hsp_num
#> 1         0         224             0           224              0            1
#>   hsps_sum_evalue hsps_product_coverage hsps_overall_identity
#> 1               0                     0                     0
#>   hsps_negative_count hsps_matches hsps_high_quality_percent_coverage
#> 1                   0            0                                  0
#>   hsps_exon_identity hsps_consensus_splices hsps_comp_adj_method
#> 1                  0                      0                    2
#>