New Benchmark for Protein Motif Alignment
Author Information
Author(s): Perrodou Emmanuel, Chica Claudia, Poch Olivier, Gibson Toby J, Thompson Julie D
Primary Institution: Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)
Hypothesis
Can multiple sequence alignment programs reliably align linear motifs in distantly related sequences?
Conclusion
None of the programs currently available can reliably align linear motifs in distantly related sequences, highlighting specific problems that need to be addressed.
Supporting Evidence
- The benchmark includes multiple alignments for most motifs annotated in the ELM resource.
- The study evaluated the accuracy of various alignment programs using the new benchmark.
- Results showed significant variability in alignment accuracy based on sequence similarity.
Takeaway
This study created a new way to test how well programs can align important parts of proteins, but found that none of them do a good job with very different proteins.
Methodology
The study developed a benchmark to assess multiple alignment methods using reference alignments of sequences with verified linear motifs.
Potential Biases
The focus on easily aligned motifs may overlook the challenges of aligning motifs in disordered regions.
Limitations
The benchmark may be biased towards known linear motifs in globular domains and does not represent all possible linear motifs, especially those in disordered regions.
Digital Object Identifier (DOI)
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