#38 · Genomics
Reusable pipelines annotate gene families, viral RNA structures and protein domains
The common thread is software that turns sequence and structural data into reusable, inspectable workflows. BAT integrates BLAST search, gene tree construction, and motif, HMM and expression annotation for phylogenomic gene family analysis across custom datasets. The plant method performs reference-free cross-species RNA-seq comparison using Pfam domain annotations from Trinity assemblies and kallisto. The viral ncRNA protocol combines automated Rfam annotation, Rfam RESTful API access, and R2DT-based 2D structure visualization within bioinformatics pipelines. These items differ in biological question and data type, so the shared element is pipeline design and programmatic reuse rather than a common data model. What is new is the packaging of multi-step annotation, retrieval and visual comparison into single local or API-accessible workflows, rather than standalone calculations. All three items are preprints, and the summaries report no benchmark results.
Preprints
De novo protein discovery in non-model organisms
Presents plant, a reference-free method that compares RNA-seq across species using Pfam protein domain annotations from Trinity assemblies and kallisto…
A novel method to select Reference Proteomes in UniProt
Proposes an MMseqs2-based clustering pipeline to select minimal, representative Reference Proteomes in UniProt across cellular and viral organisms, reducing…
Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes
Uses MMseqs2 clustering of bacterial proteomes to define core protein sets and flags length-outlier proteins as likely frame-shift or start-codon artifacts,…
Topic history
| Date | Rank |
|---|---|
| #38 | |
| #34 | |
| #39 | |
| #37 | |
| #32 |