orf_locate

Extracts ORF identifiers, start/end positions and strand
orientation directly from the FASTA headers produced by
Prodigal. The resulting table is ready for downstream
gene-cluster analyses.

Performs end-to-end analysis of gene clusters—such as photosynthesis,
carbon/nitrogen/sulfur cycling, carotenoid, antibiotic, or viral marker genes
(e.g., capsid, polymerase, integrase)—from genomes and metagenomes.
It parses Basic Local Alignment Search Tool (BLAST) results in tab-delimited
format produced by tools like NCBI BLAST+ and Diamond BLASTp, filters
Open Reading Frames (ORFs) by length, detects contiguous clusters of reference genes,
optionally extracts genomic coordinates, merges functional annotations, and
generates publication-ready arrow plots. The package works seamlessly with
or without the coding sequences input and skips plotting when no functional
groups are found. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Liuyang Li

gclink

Gene-Cluster Discovery, Annotation and Visualization

orf_locate function

<dl><dt>in_seq_data</dt>
<dd>A data frame with two columns:<dl>
<dt><code>SeqName</code></dt>
<dd>ORF identifier (Prodigal format: <code>&gt;ORF_id # start # end # strand # ...</code>).</dd></dl></dd><dt><code>Sequence</code></dt>
<dd>ORF sequence.</dd>
</dl>Example:
<code>"Kuafubacteriaceae--GCA_016703535.1---JADJBV010000001.1_1 # 74 # 1018 # 1 # ..."</code>
Can be imported from Prodigal FASTA using:
<div class="sourceCode r"></div><pre><code>seq_data &lt;- Biostrings::readBStringSet("Prodigal.fasta",format="fasta", nrec=-1L, skip=0L, seek.first.rec=FALSE, use.names=TRUE) %&gt;%
 data.frame(Sequence = .) %&gt;%
 tibble::rownames_to_column("SeqName")
</code></pre>

Arguments

Parse ORF Coordinates from Prodigal FASTA Headers — orf_locate

<dl>

<dt>in_seq_data</dt>
<dd>A data frame with two columns:<dl>
<dt><code>SeqName</code></dt>
<dd>ORF identifier (Prodigal format: <code>&gt;ORF_id # start # end # strand # ...</code>).</dd>

<dt><code>Sequence</code></dt>
<dd>ORF sequence.</dd>


</dl>Example:
<code>"Kuafubacteriaceae--GCA_016703535.1---JADJBV010000001.1_1 # 74 # 1018 # 1 # ..."</code>
Can be imported from Prodigal FASTA using:
<div class="sourceCode r"><pre><code>seq_data &lt;- Biostrings::readBStringSet("Prodigal.fasta",format="fasta", nrec=-1L, skip=0L, seek.first.rec=FALSE, use.names=TRUE) %&gt;%
 data.frame(Sequence = .) %&gt;%
 tibble::rownames_to_column("SeqName")
</code></pre></div></dd>

</dl>

orf_locate: Parse ORF Coordinates from Prodigal FASTA Headers

Description

Usage

Value

Arguments