aafile2rbhplus: aafile2rbhplus

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

aafile2rbhplus

Description

This function calculates (conditional-)reciprocal best hit (CRBHit) pairs from two AA fasta files. Conditional-reciprocal best hit pairs were introduced by Aubry S, Kelly S et al. (2014). Sequence searches are performed with last Kiełbasa, SM et al. (2011) [default] or with mmseqs2 Steinegger, M and Soeding, J (2017) or with diamond Buchfink, B et al. (2021). If one specifies aafile1 and aafile2 as the same input a selfblast is conducted.

Usage

aafile2rbhplus(
  aafile1,
  aafile2,
  dbfile1 = NULL,
  dbfile2 = NULL,
  searchtool = "last",
  lastpath = paste0(find.package("CRBHits"), "/extdata/last-1595/bin/"),
  lastD = 1e+06,
  lastm = 10,
  mafconvertpath = paste0(find.package("CRBHits"), "/extdata/maf-convert-crbhits"),
  mmseqs2path = NULL,
  mmseqs2sensitivity = 5.7,
  mmseqs2maxseqs = 300,
  diamondpath = NULL,
  diamondsensitivity = "--sensitive",
  diamondmaxtargetseqs = 0,
  lambda3path = NULL,
  lambda3sensitivity = "sensitive",
  lambda3nummatches = 25,
  outpath = "/tmp",
  crbh = TRUE,
  keepSingleDirection = FALSE,
  eval = 0.001,
  qcov = 0,
  tcov = 0,
  pident = 0,
  alnlen = 0,
  rost1999 = FALSE,
  filter = NULL,
  plotCurve = FALSE,
  fit.type = "mean",
  fit.varweight = 0.1,
  fit.min = 5,
  threads = 1,
  aafile2tmp = TRUE,
  remove = TRUE,
  remove.db = TRUE
)

Arguments

aafile1	aa1 fasta file [mandatory]
aafile2	aa2 fasta file [mandatory]
dbfile1	aa1 db file [optional]
dbfile2	aa2 db file [optional]
searchtool	specify sequence search algorithm last, mmseqs2, diamond or lambda3 [default: last]
lastpath	specify the PATH to the last binaries [default: /extdata/last-1595/bin/]
lastD	last option D: query letters per random alignment [default: 1e6]
lastm	last option m: maximum initial matches per query position [default: 10]
mafconvertpath	specify the PATH to the maf-convert script [default: /extdata/maf-convert-crbhits]
mmseqs2path	specify the PATH to the mmseqs2 binaries [default: NULL]
mmseqs2sensitivity	specify the sensitivity option of mmseqs2 [default: 5.7]
mmseqs2maxseqs	mmseqs2 option: Maximum results per query sequence allowed to pass the prefilter [default: 300]
diamondpath	specify the PATH to the diamond binaries [default: NULL]
diamondsensitivity	specify the sensitivity option of diamond [default: –sensitive]
diamondmaxtargetseqs	specify the maximum number of target sequences per query option of diamond [default: 0]
lambda3path	specify the PATH to the lambda3 binaries [default: NULL]
lambda3sensitivity	specify the sensitivity option of lambda3 [default: sensitive]
lambda3nummatches	specify the number of matches per query option of lambda3 [default: 25]
outpath	specify the output PATH [default: /tmp]
crbh	specify if conditional-reciprocal hit pairs should be retained as secondary hits [default: TRUE]
keepSingleDirection	specify if single direction secondary hit pairs should be retained [default: FALSE]
eval	evalue [default: 1e-3]
qcov	query coverage [default: 0.0]
tcov	target coverage [default: 0.0]
pident	percent identity [default: 0.0]
alnlen	alignment length [default: 0.0]
rost1999	specify if hit pairs should be filter by equation 2 of Rost 1999 [default: FALSE]
filter	specify additional custom filters as list to be applied on hit pairs [default: NULL]
plotCurve	specify if crbh fitting curve should be plotted [default: FALSE]
fit.type	specify if mean or median should be used for fitting [default: mean]
fit.varweight	factor for fitting function to consider neighborhood [default: 0.1]
fit.min	specify minimum neighborhood alignment length [default: 5]
threads	number of parallel threads [default: 1]
aafile2tmp	specify if aa input files sequenceIDs should be reduced to the first word and be written to a temporary aa file [default: TRUE]
remove	specify if last result files should be removed [default: TRUE]
remove.db	specify if last db files should be removed [default: TRUE]

Value

List of three (crbh=FALSE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query

List of four (crbh=TRUE)
1: $crbh.pairs
2: $crbh1 matrix; query > target
3: $crbh2 matrix; target > query
4: $rbh1_rbh2_fit; evalue fitting function

Author(s)

Kristian K Ullrich

References

Aubry S, Kelly S et al. (2014) Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis. PLOS Genetics, 10(6) e1004365.

Kiełbasa, SM et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome research, 21(3), 487-493.

Rost B. (1999). Twilight zone of protein sequence alignments. Protein Engineering, 12(2), 85-94.

See Also

aa2rbh

Examples

## compile last-1595 within CRBHits
CRBHits::make_last()
## load example sequence data
athfile <- system.file("fasta", "ath.aa.fasta.gz", package="CRBHits")
alyfile <- system.file("fasta", "aly.aa.fasta.gz", package="CRBHits")
## get CRBHit pairs
ath_aly_crbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=alyfile,
    plotCurve=TRUE)
dim(ath_aly_crbh$crbh.pairs)
## get classical reciprocal best hit (RBHit) pairs
ath_aly_rbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=alyfile,
    crbh=FALSE)
dim(ath_aly_rbh$crbh.pairs)
## selfblast
ath_selfblast_crbh <- aafile2rbhplus(
    aafile1=athfile,
    aafile2=athfile,
    plotCurve=TRUE)
## see ?cds2rbh for more examples

kullrich/CRBHits documentation built on Nov. 13, 2024, 7:44 a.m.