Lift&Add
Fuente:
Zenodo
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Recurso digital |
| Veröffentlicht: |
Zenodo
2026
|
| Schlagworte: | |
| Online-Zugang: | |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| _version_ | 1866901743612198912 |
|---|---|
| author | Shukla, Navya Gallego Romero, Irene |
| author_facet | Shukla, Navya Gallego Romero, Irene |
| contents | <p>Archived code for Lift&Add - rapid and robust addition of new species to alignments of conserved non-coding sequences. </p> <p>https://www.biorxiv.org/content/10.1101/2025.10.14.682260v1</p> <p>From abstract: <br><br>Identifying sequence constraint across long evolutionary distances is a powerful method for the discovery of functional genomic sequences, especially putative non-coding elements. Conserved elements have been a mainstay of comparative genomic research, and can be further investigated for species-specific sequence acceleration to dissect the genetic basis of trait evolution. The conclusions of these comparative genomic studies are contingent on the number and range of species included in this phylogenetic analysis. However, while the number of metazoan genomes sequences is increasing rapidly, adding new genomes to existing whole-genome alignments remains computationally expensive. Here, we present a bioinformatic workflow, Lift\&Add, that enables conserved elements, coding or non-coding, to be rapidly mapped to new genomes ("Lift") and subsequently be added to pre-existing multiple species alignments ("Add"), thus providing an avenue for easy exploration of these putative functional elements. Focusing here on a group of species that has been largely under-represented in genomic comparisons, the marsupials, we demonstrate the intuition behind this workflow and provide an example comparative genomic analysis that can be performed. </p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_19568005 |
| institution | Zenodo |
| language | |
| publishDate | 2026 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Lift&Add Shukla, Navya Gallego Romero, Irene Genomics/methods <p>Archived code for Lift&Add - rapid and robust addition of new species to alignments of conserved non-coding sequences. </p> <p>https://www.biorxiv.org/content/10.1101/2025.10.14.682260v1</p> <p>From abstract: <br><br>Identifying sequence constraint across long evolutionary distances is a powerful method for the discovery of functional genomic sequences, especially putative non-coding elements. Conserved elements have been a mainstay of comparative genomic research, and can be further investigated for species-specific sequence acceleration to dissect the genetic basis of trait evolution. The conclusions of these comparative genomic studies are contingent on the number and range of species included in this phylogenetic analysis. However, while the number of metazoan genomes sequences is increasing rapidly, adding new genomes to existing whole-genome alignments remains computationally expensive. Here, we present a bioinformatic workflow, Lift\&Add, that enables conserved elements, coding or non-coding, to be rapidly mapped to new genomes ("Lift") and subsequently be added to pre-existing multiple species alignments ("Add"), thus providing an avenue for easy exploration of these putative functional elements. Focusing here on a group of species that has been largely under-represented in genomic comparisons, the marsupials, we demonstrate the intuition behind this workflow and provide an example comparative genomic analysis that can be performed. </p> |
| title | Lift&Add |
| topic | Genomics/methods |
| url | https://doi.org/10.5281/zenodo.19568005 |