Skip to content

Commit

Permalink
Update 'getstarted.md' to clarify NaiveFinder algorithm details and O…
Browse files Browse the repository at this point in the history
…RFI structure
  • Loading branch information
camilogarciabotero committed Oct 30, 2024
1 parent 05d5da5 commit 4beee1c
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions docs/src/getstarted.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
## Finding complete and overlapped ORFIs

The main function in the GeneFinder package is `findorfs`, which serves as an interface to various gene-finding algorithms. By default, `findorfs` uses a `NaiveFinder` algorithm, a simple approach that detects all non-outbounded Open Reading Frames (ORFs) in a DNA sequence. You can also specify a different algorithm by setting the `finder` keyword argument. For more details on the NaiveFinder algorithm, see [NaiveFinder](https://camilogarciabotero.github.io/GeneFinder.jl/dev/api/#GeneFinder.NaiveFinder-Union{Tuple{Union{BioSequences.LongDNA{N},%20BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}},%20Tuple{N}}%20where%20N) documentation for more details.
The main function in the GeneFinder package is `findorfs`, which serves as an interface to various gene-finding algorithms. By default, `findorfs` uses a `NaiveFinder` algorithm, a simple approach that detects all non-outbounded Open Reading Frames (ORFs) in a DNA sequence. You can also specify a different algorithm by setting the `finder` keyword argument. For more details on the NaiveFinder algorithm, see [NaiveFinder](https://camilogarciabotero.github.io/GeneFinder.jl/dev/api#GeneFinder.NaiveFinder-Union{Tuple{Union{BioSequences.LongDNA{N},%20BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}},%20Tuple{N}}%20where%20N) documentation for more details.

!!! note
The minlen keyword argument in `NaiveFinder` is set to a minimum length of 6 nucleotides (nt). As a result, it may identify short ORFs that aren't necessarily genes, such as dna"ATGTGA" producing the amino acid sequence aa"M*".
Expand Down Expand Up @@ -35,7 +35,7 @@ orfs = findorfs(seq, finder=NaiveFinder) # use finder=NaiveCollector as an alter

## Extracting Sequences from ORFIs

The `ORFI` structure displays the location, frame, and strand, but currently does not include the sequence *per se*. To extract the sequence of an `ORFI` instance, you can use the `sequence` method directly on it, or you can also broadcast it over the `orfs` collection using the dot syntax `.`:
The `ORFI` structure displays the location, frame, and strand, and other fields (see more about the [OpenReadingFrameInterval struct](https://camilogarciabotero.github.io/GeneFinder.jl/dev/orftype#The-ORFI-type)). To extract the sequence of an `ORFI` instance, you can use the `sequence` method directly on it, or you can also broadcast it over the `orfs` collection using the dot syntax `.`:

```julia
julia> sequence.(orfs)
Expand Down

0 comments on commit 4beee1c

Please sign in to comment.