Infer orthologous lncRNAs between multiple species

Inference of orthologous lncRNAs between multiple species is performed via pairwise BLAST (reciprocal) best hit comparisons. The corresponding orthologous tables are then stored in an output folder.

map_generator_lnc(
  query_file,
  subjects_folder,
  output_folder,
  task = "blastn",
  eval = "1E-5",
  ortho_detection = "RBH",
  max.target.seqs = 10000,
  min_qry_coverage_hsp = 30,
  min_qry_perc_identity = 30,
  logical_connective = "AND",
  min_alig_length = NULL,
  comp_cores = 1,
  progress_bar = TRUE,
  sep = ";",
  path = NULL,
  ...
)

Arguments

query_file

a character string specifying the path to the lncRNAs file of the query organism in fasta format.

subjects_folder

a character string specifying the path to the folder where lncRNAs files in fasta format of the subject organisms are stored.

output_folder

a character string specifying the path to the folder where output orthologous tables should be stored.

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 character string specifying the e-value for BLAST based orthology inference. Please use the scientific notation.

ortho_detection

a character string specifying the Orthology Inference method that shall be used to perform dNdS computations. Possible options are:

• ortho_detection = "BH": BLAST best unidirectional hit

• ortho_detection = "RBH": BLAST best reciprocal 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 .

min_qry_coverage_hsp

minimum qcovhsp (= query coverage of the HSP) of an orthologous hit (a value between 1 and 100).

min_qry_perc_identity

minimum perc_identity (= percent sequence identity between query and selected HSP) of an orthologous hit (a value between 1 and 100).

logical_connective

character representing logical connective (either "AND" or "OR") if min_alig_length is not NULL filtering is done on min_alig_length and/or min_qry_perc_identity

min_alig_length

minimum alig_length (alignment length) to an orthologous hit (number of aligned nucleotides or amino acids depending on the input data)

comp_cores

number of computing cores that shall be used to perform parallelized computations.

progress_bar

should a progress bar be shown. Default is progress_bar = TRUE.

sep

a file separator that is used to store maps as csv file.

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.

...

additional parameters that shall be passed to dNdS.

Details

Given a query organism and a set of subject organsisms that are stored in the same folder, this function crawls through all subject organsism and infers the lncRNA homologs in pairwise species comparisons.

Note

According to Sarropoulos, I., et al. (2019) orthology detection of lncRNAs was performed by reciprocal BLAST searches. Significant hits with an e-value <= 10-3 were selected having an alignment identity >= 10% OR a minimum alignment length >= 50 nucleotides.

References

Sarropoulos I, Marin R, Cardoso-Moreira M, Kaessmann H (2019). “Developmental dynamics of lncRNAs across mammalian organs and species.” Nature, 571, 510--514.

Author

Hajk-Georg Drost

Examples

if (FALSE) {
# example using classic blastn searches
map_generator_lnc(
   query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
   subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
   output_folder   = "orthologs_lncrna",
   comp_cores      = 1
)
# example using  discontiguous megablast used to find somewhat distant sequences
map_generator_lnc(
   query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
   subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
   output_folder   = "orthologs_lncrna",
   task            = "dc-megablast",
   comp_cores      = 1
)
}

if (FALSE) {
# parameter settings based on Sarropoulos, I., et al. (2019)
map_generator_lnc(
   query_file,,
   subjects_folder,
   eval                  = 1E-3,
   ortho_detection       = "RBH",
   output_folder,
   min_qry_coverage_hsp  = 0,
   min_qry_perc_identity = 10,
   logical_connective    = "OR",
   min_alig_length       = 50)
}