Orthology Inference of lncRNAs

This function takes nucleotide or protein sequences for a set of organisms and performs orthology inference to detect orthologous genes within the given organisms based on selected orthology inference programs.

This function takes nucleotide or protein sequences for a set of organisms and performs orthology inference to detect orthologous genes within the given organisms based on selected orthology inference programs.

orthologs_lnc(
  query_file,
  subject_file,
  task = "blastn",
  eval = "1E-5",
  ortho_detection = "RBH",
  max.target.seqs = 10000,
  output.path = getwd(),
  comp_cores = 1,
  path = NULL
)

orthologs_lnc(
  query_file,
  subject_file,
  task = "blastn",
  eval = "1E-5",
  ortho_detection = "RBH",
  max.target.seqs = 10000,
  output.path = getwd(),
  comp_cores = 1,
  path = NULL
)

Arguments

query_file

a character string specifying the path to the sequence file of interest (query organism).

subject_file

a character string specifying the paths to the sequence files of interest (subject organisms).

task

nucleotide search task option. Options are:

• task = "blastn" : Standard nucleotide-nucleotide comparisons (default) - Traditional BLASTN requiring an exact match of 11.

• task = "blastn-short" : Optimized nucleotide-nucleotide comparisons for query sequences shorter than 50 nucleotides.

• task = "dc-megablast" : Discontiguous megablast used to find somewhat distant sequences.

• task = "megablast" : Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences.

• task = "rmblastn"

eval

a numeric value specifying the E-Value cutoff for BLAST hit detection.

ortho_detection

a character string specifying the orthology inference method that shall be performed to detect orthologous genes. Options are:

• ortho_detection = "RBH" (BLAST reciprocal best hit) (Default)

• ortho_detection = "BH" (BLAST best hit)

max.target.seqs

a numeric value specifying the number of aligned sequences to keep. Please be aware that max.target.seqs selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 .

output.path

path to which output shall be stored.

comp_cores

a numeric value specifying the number of cores to be used for multicore computations.

path

a character string specifying the path to the corresponding orthology inference tool. For "BH" and "RBH": path to BLAST, "PO": path to ProteinOrtho 5.07, "OrthoMCL": path to OrthoMCL.

Value

A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes in the second column and the amino acid sequences in the third column.

A data.table storing the query_ids of orthologous genes in the first column, the subject_ids of orthologous genes in the second column and the amino acid sequences in the third column.

Details

This function takes sequence files of a query organism and a subject organism and performs orthology inference using a defined orthology inference method to dectect orthologous genes.

The following interfaces are implemented in the orthologs function:

BLAST based methods:

• BLAST best hit (BH)

• BLAST reciprocal best hit (RBH)

This function takes sequence files of a query organism and a subject organism and performs orthology inference using a defined orthology inference method to dectect orthologous genes.

The following interfaces are implemented in the orthologs function:

BLAST based methods:

• BLAST best hit (BH)

• BLAST reciprocal best hit (RBH)

References

BLAST: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml

ProteinOrtho: https://www.bioinf.uni-leipzig.de/Software/proteinortho/

BLAST: http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml

ProteinOrtho: https://www.bioinf.uni-leipzig.de/Software/proteinortho/

See also

blast_rec, dNdS

blast_rec, dNdS

Author

Hajk-Georg Drost

Examples

if (FALSE) {

### BLAST Reciprocal Best Hit
# perform orthology inference using BLAST reciprocal best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file   = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "RBH")
          
          
### BLAST Best Hit
# perform orthology inference using BLAST best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "BH")


# multicore version          
orthologs.lnc(query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file   = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "RBH", 
          comp_cores      = 2)          
          
          
          
}
if (FALSE) {

### BLAST Reciprocal Best Hit
# perform orthology inference using BLAST reciprocal best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file   = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "RBH")
          
          
### BLAST Best Hit
# perform orthology inference using BLAST best hit
# and fasta sequence files storing protein sequences
orthologs.lnc(query_file = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "BH")


# multicore version          
orthologs.lnc(query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
          subject_file   = system.file('seqs/ortho_lyra_cds.fasta', package = 'orthologr'),
          ortho_detection = "RBH", 
          comp_cores      = 2)          
          
          
          
}