m_slicer: generate proteins with alternative translation start sites

In gogleva/SecretSanta: flexible pipelines for secretome prediction

Description

NB: this is an experimental option.

This function generates all possible subsequences (slices) starting with methionines (M). This might be usefull when translation start sites assumed to be mis-predicted for some of the provided proteins. For example, in cases when the set is obtained after de novo genome or transcriptome assembly.

Output of this step can be used as an input for secretome prediction pipeline to rescue secreted proteins with potentially mis-predicted start sites. Please proceed with caution.

Usage

m_slicer(input_obj, min_len, run_mode = c("slice", "rescue"))

Arguments

input_obj	an instance of CBSResult class or AAStringSet class containing protein sequences as on of the attributes
min_len	sliced sequences below this threshold will be discarded
run_mode	slice - just slice input fasta, regardless of its origin; rescue - get proteins not predicted to be secreted on the initial run, generate slices;

Value

a set of sliced sequences, AAStringSet object

Examples

# Example 1: generate proteins with alterative translation start site for
# AAStringSet object
aa <- readAAStringSet(system.file("extdata","sample_prot_100.fasta",
package = "SecretSanta"))
m_slicer(aa[1:10], 100, run_mode = 'slice')

# Example 2: generate proteins with alterative translation start site for
# CBSResult object
inp <- CBSResult(in_fasta = aa[1:10])
s1_sp2 <- signalp(inp, version = 2, organism = 'euk',
run_mode = "starter", legacy_method = 'hmm')
slices <- m_slicer(s1_sp2, min_len = 100, run_mode = 'rescue')
inp_slices <- CBSResult(in_fasta = slices)
s2_sp2_rescue <- signalp(inp_slices, version = 2, organism = 'euk',
run_mode = 'starter', legacy_method = 'hmm')

gogleva/SecretSanta documentation built on May 30, 2019, 8:02 a.m.