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Seamless Integration of BLAST Sequence Searches in R

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@HajkD HajkD released this 10 Sep 12:42
v0.3.2
02dad6d

This package provides interface functions for users to perform local Basic Local Alignment Search Tool (BLAST) searches. The search results can be efficiently imported into the R session.

Interfaces implemented in metablastr:

Perform BLAST searches

  • blast_protein_to_protein(): Perform Protein to Protein BLAST Searches (BLASTP)
  • blast_nucleotide_to_nucleotide(): Perform Nucleotide to Nucleotide BLAST Searches (BLASTN)
  • blast_nucleotide_to_protein(): Perform Nucleotide to Protein BLAST Searches (BLASTX)
  • blast_protein_to_nucleotide(): Perform Protein to Nucleotide BLAST Searches (TBLASTN)
  • blast_best_hit(): Retrieve only the best BLAST hit for each query
  • blast_best_reciprocal_hit(): Retrieve only the best reciprocal BLAST hit for each query
  • blast_rpsblast: Perform Reverse PSI-BLAST searches (rpsblast)
  • read_blast(): Import BLAST output into R session (in memory) or via PostgresSQL database connection.

BLAST against common NCBI databases

  • blast_protein_to_nr_database(): Perform Protein to Protein BLAST Searches against the NCBI non-redundant database
  • blast_nt(): Perform Nucleotide to Nucleotide BLAST Searches against the NCBI non-redundant database
  • blast_est(): Perform Nucleotide to Nucleotide BLAST Searches against the NCBI expressed sequence tags database
  • blast_pdb_protein():
  • blast_pdb_nucleotide():
  • blast_swissprot():
  • blast_delta():
  • blast_refseq_rna():
  • blast_refseq_gene():
  • blast_refseq_protein():

BLAST against a set of organisms

  • blast_nucleotide_to_genomes(): Perfrom BLAST Searches Against a Set of Genomes
  • blast_protein_to_proteomes(): Perfrom BLAST Searches Against a Set of Proteomes
  • detect_homologs_cds_to_cds(): Perform CDS to CDS BLAST Searches against a set of CDS files
  • detect_homologs_proteome_to_proteome(): Perform Proteome to Proteome BLAST Searches against a set of Proteomes
  • extract_hit_seqs_from_genomes(): Extract sequences of BLAST hits in respective genomes and store it as 'fasta' file(s)
  • extract_random_seqs_from_genome(): Extract random loci from a genome of interest
  • sample_chromosome_intervals(): Helper function to sample random intervals of length 'interval_width' from chromosomes

Analyze BLAST Report

  • filter_blast_:

Navigation functions

  • list_outformats(): List available BLAST output formats
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