Merge pull request #37 from camilogarciabotero/rbs

Ribosome Binding Sites motifs

Author: camilogarciabotero

docs/Manifest.toml

@@ -1,6 +1,6 @@
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docs/make.jl

@@ -18,6 +18,7 @@ pgs = [
         "The ORF type" => "orftype.md",
         "Scoring ORFs" => "features.md",
         "A Simple Coding Rule" => "simplecodingrule.md",
+        "Ribosome Binding Sites" => "rbs.md",
         "Writing ORFs In Files" => "iodocs.md",
     ],
     "API" => "api.md",

docs/src/rbs.md

@@ -0,0 +1,82 @@
+## Ribosome Binding Site (RBS) Motifs
+
+This document provides information on Ribosome Binding Site (RBS) motifs based on the Prodigal paper. The RBS motifs are categorized by spacer ranges, which indicate the number of base pairs (bp) between the RBS and the start codon.
+
+### Spacer Ranges and Representative RBS Motifs
+
+Example sequence with RBS motif:
+
+ Spacer Range | Representative RBS Motif(s)
+ ------------ | ---------------------------
+ 3-4 bp       | GGA, GAG, AGG, AGxAG, AGGAG
+ 5-10 bp      | GGAG, GAGG, GGxGG, AGGAGG
+ 11-12 bp     | GGA, GAG, AGG, AGxAG, AGGAG
+ 13-15 bp     | GGA, GAG, AGG, AGGA, AGGAG
+
+### Window Checking Ranges
+
+Three different window checking ranges are defined to identify potential RBS motifs relative to the start codon (ATG):
+
+- Window Checking A:
+```
+                 -10    -3  |-> start codon
+               ...|......|..ATG...
+```
+
+- Window Checking B:
+```
+           -16        -5    |-> start codon
+         ...|..........|....ATG...
+```
+
+- Window Checking C:
+```
+       -20      -11         |-> start codon
+       .|........|..........ATG...
+```
+
+### RBS Motif Scoring
+
+The RBS motif scoring is based on the Prodigal paper, which uses a scoring system to identify potential RBS motifs. The scoring system is as follows:
+
+
+
+### Example
+
+An example of an exact search query for an RBS motif is provided:
+
+- **ExactSearchQuery(dna"ATACG", iscompatible)** returns 5, indicating the position of the motif.
+
+```
+       -20  -15  -10  -5    |-> start codon
+        |....|....|....|....ATG...
+                  GGAGGACCCCATGACACACACAACAC  
+                  |----|:RBS(dna"GGAGGA", 1:5, :A, 27, STRAND_POS)
+```
+
+To inspect the RBS motifs of a given ORF, we can use the `_findrbs` function. This function returns the RBS motifs of a given ORF:
+
+```julia
+
+phi = dna"GTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGT ACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGA"
+
+orf = findorfs(phi)[3]
+
+GeneFinder._findrbs(orf)
+
+6-element Vector{RBS}:
+ RBS(GAG, 90:92, :A, 13, STRAND_POS)
+ RBS(GGAG, 89:92, :B, 16, STRAND_POS)
+ RBS(AGG, 88:90, :B, 13, STRAND_POS)
+ RBS(GGA, 89:91, :B, 13, STRAND_POS)
+ RBS(GAG, 90:92, :B, 13, STRAND_POS)
+ RBS(AGGA, 88:91, :B, 16, STRAND_POS)
+
+```
+
+Now, following the scoring scheme mentioned above, we can calculate the RBS score for each motif. This criteria is implemented in the `orf_rbs_score` or simply aliased to `orbs` function:
+
+```julia
+orf_rbs_score(orf)
+29
+```

src/GeneFinder.jl

@@ -21,7 +21,10 @@ using BioSequences:
     reverse_complement,
     randdnaseq,
     ncbi_trans_table,
-    translate
+    translate,
+
+    ExactSearchQuery,
+    iscompatible
 
 using BioMarkovChains: BioMarkovChain, ECOLICDS, ECOLINOCDS, log_odds_ratio_score
 using IterTools: takewhile, iterated
@@ -31,19 +34,21 @@ using GenomicFeatures: GenomicFeatures, AbstractGenomicInterval, Strand, summary
 include("algorithms/naivefinder.jl")
 include("algorithms/naivecollector.jl")
 
-# Coding Criteria
-include("criteria/lordr.jl")
-
 # Main functions
 include("types.jl")
 include("findorfs.jl")
-include("iscoding.jl")
 include("io.jl")
 
 # Utils and extended functions
 include("utils.jl")
 include("extended.jl")
 
+# RBS Scoring
+include("rbs.jl")
+
+# Coding Criteria
+include("criteria.jl")
+
 # Precompiled workloads
 include("workload.jl")
 

src/criteria/lordr.jl src/criteria.jlsrc/criteria/lordr.jl renamed to src/criteria.jl

@@ -1,4 +1,38 @@
-export log_odds_ratio_decision_rule, lordr #lors
+export iscoding,
+    log_odds_ratio_decision_rule, lordr,
+    ribsome_binding_site_decision_rule, rbsdr
+
+
+    @doc raw"""
+    iscoding(orf::ORFI{N,F}; criteria::Function = lordr, kwargs...) -> Bool
+
+Check if the given DNA sequence of an ORF is likely to be coding based on a scoring scheme/function.
+
+## Scoring Criteria/Functions
+- `lordr`: Log-Odds Ratio Decision Rule
+- `rbsdr`: Ribosome Binding Site Decision Rule
+
+```
+phi = dna"GTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAAT...AGTGTTTCCAGTCCGTTCAGTTAATAGTCAGGTTAAAGATAAAAGATTGA"
+orfs = findorfs(phi)
+
+orf = orfs[2]
+    ORFI{NaiveFinder}(94:126, '-', 1)
+
+iscoding(orf)  # Returns: true
+```
+"""
+function iscoding(
+    orf::ORFI{N,F};
+    criteria::Function = lordr, #rbsdr
+    kwargs...
+) where {N,F<:GeneFinderMethod}
+    return criteria(orf; kwargs...)
+end
+
+### Actual criteria functions ###
+
+## Log-Odds Ratio Decision Rule
 
 @doc raw"""
     log_odds_ratio_decision_rule(
@@ -41,15 +75,15 @@ iscoding(sequence)  # Returns: true or false
 ```
 """
 function lordr( #log_odds_ratio_decision, also lordr/cudr/kfdr/aadr
-    sequence::NucleicSeqOrView{DNAAlphabet{N}};
+    orf::ORFI{N,F};
     modela::BioMarkovChain = ECOLICDS,
     modelb::BioMarkovChain = ECOLINOCDS,
     b::Number = 2,
     η::Float64 = 5e-3
-) where {N}
-
-    scorea = log_odds_ratio_score(sequence; modela=modela, b=b)
-    scoreb = log_odds_ratio_score(sequence; modela=modelb, b=b)
+) where {N,F<:GeneFinderMethod}
+    orfseq = sequence(orf)
+    scorea = log_odds_ratio_score(orfseq; modela=modela, b=b)
+    scoreb = log_odds_ratio_score(orfseq; modela=modelb, b=b)
 
     logodds = scorea / scoreb
 
@@ -60,4 +94,33 @@ function lordr( #log_odds_ratio_decision, also lordr/cudr/kfdr/aadr
     end
 end
 
-const log_odds_ratio_decision_rule = lordr # criteria
+const log_odds_ratio_decision_rule = lordr # criteria
+
+## Ribosome Binding Site Decision Rule
+
+"""
+    ribsome_binding_site_decision_rule(orf::ORFI{N,F}) where {N,F<:GeneFinderMethod} -> Bool
+
+Evaluates if an Open Reading Frame (ORF) has a significant ribosome binding site (RBS).
+
+The function uses the `orf_rbs_score` to calculate a score for the ORF's RBS region and returns
+true if the score exceeds a threshold of 9, indicating the presence of at least one RBS.
+
+# Arguments
+- `orf::ORFI{N,F}`: An Open Reading Frame Interface (ORFI) object parameterized by N and F,
+  where F is a subtype of GeneFinderMethod
+
+# Returns
+- `Bool`: `true` if the RBS score is greater than 9, `false` otherwise
+
+"""
+function rbsdr(orf::ORFI{N,F}) where {N,F<:GeneFinderMethod}
+    scr = orf_rbs_score(orf)
+    if scr > 9 # at least one RBS...
+        return true
+    else
+        return false
+    end
+end
+
+const ribsome_binding_site_decision_rule = rbsdr

src/extended.jl

@@ -14,9 +14,9 @@ import BioSequences: translate
 
 ## Methods from BioMarkovChains that expand their fuctions to this package structs
 import BioMarkovChains: log_odds_ratio_score
-export log_odds_ratio_score, lors
+# export log_odds_ratio_score, lors
 
 @inline log_odds_ratio_score(orf::ORFI{N,F}; kwargs...) where {N,F} = log_odds_ratio_score(sequence(orf); kwargs...)
-@inline log_odds_ratio_decision_rule(orf::ORFI{N,F}; kwargs...) where {N,F} = log_odds_ratio_decision_rule(sequence(orf); kwargs)
+# @inline log_odds_ratio_decision_rule(orf::ORFI{N,F}; kwargs...) where {N,F} = log_odds_ratio_decision_rule(sequence(orf); kwargs)
 
-const  lors = log_odds_ratio_score
+# const  lors = log_odds_ratio_score