blastp_df

A dataset containing BLASTP alignment results for proteins from test genomes of bacteria,
including alignment metrics.

datasets

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

blastp_df function

A data frame with multiple rows and 12 variables:<dl>
<dt>qaccver</dt>
<dd>Character. Protein query identifier.</dd><dt>saccver</dt>
<dd>Character. Subject protein identifier from reference databases.</dd><dt>pident</dt>
<dd>Numeric. Percentage identity between query and subject sequences.</dd><dt>length</dt>
<dd>Numeric. Length of the aligned sequence region.</dd><dt>mismatch</dt>
<dd>Numeric. Number of mismatches in the alignment.</dd><dt>gapopen</dt>
<dd>Numeric. Number of gap openings in the alignment.</dd><dt>qstart</dt>
<dd>Numeric. Start position in query sequence.</dd><dt>qend</dt>
<dd>Numeric. End position in query sequence.</dd><dt>sstart</dt>
<dd>Numeric. Start position in subject sequence.</dd><dt>send</dt>
<dd>Numeric. End position in subject sequence.</dd><dt>evalue</dt>
<dd>Numeric. Expect value for the alignment.</dd><dt>bitscore</dt>
<dd>Numeric. Bit score for the alignment.</dd>
</dl>

Format

BLASTP Results for test Proteins — blastp_df

A data frame with multiple rows and 12 variables:<dl>
<dt>qaccver</dt>
<dd>Character. Protein query identifier.</dd>

<dt>saccver</dt>
<dd>Character. Subject protein identifier from reference databases.</dd>

<dt>pident</dt>
<dd>Numeric. Percentage identity between query and subject sequences.</dd>

<dt>length</dt>
<dd>Numeric. Length of the aligned sequence region.</dd>

<dt>mismatch</dt>
<dd>Numeric. Number of mismatches in the alignment.</dd>

<dt>gapopen</dt>
<dd>Numeric. Number of gap openings in the alignment.</dd>

<dt>qstart</dt>
<dd>Numeric. Start position in query sequence.</dd>

<dt>qend</dt>
<dd>Numeric. End position in query sequence.</dd>

<dt>sstart</dt>
<dd>Numeric. Start position in subject sequence.</dd>

<dt>send</dt>
<dd>Numeric. End position in subject sequence.</dd>

<dt>evalue</dt>
<dd>Numeric. Expect value for the alignment.</dd>

<dt>bitscore</dt>
<dd>Numeric. Bit score for the alignment.</dd>


</dl>

blastp_df: BLASTP Results for test Proteins

Description

Usage

Arguments

Format