Are there any open and freely distributed standard datasets for testing new algorithms for multiple sequence alignment?

  • $\begingroup$ possible duplicate of What is the state-of-the-art algorithm for multiple sequence alignment? $\endgroup$ – Devashish Das Jul 30 '14 at 11:17
  • $\begingroup$ Welcome to Biology Beta @msa!!! Thanks for asking the wonderful question but I suggest you close any on one of ones you asked as they are duplicate of each other. $\endgroup$ – Devashish Das Jul 30 '14 at 11:18
  • $\begingroup$ I have always myself wondered about this so it would be great to get a detailed response! but for the moment, could you not look at a known protein or DNA sequence like Ras within a organism or different species and align them? The best way to do it is to go to UniProt (uniprot.org) and type in a protein such as Ras. Once you select a particular Ras, then under the phylogenomic databases you can select OrthoDB and once you enter the page you can select get FASTA or Tab delimited on the top of the page! $\endgroup$ – Behzad Rowshanravan Jul 30 '14 at 11:25
  • $\begingroup$ @DevashishDas This question is not a duplicate of the linked question as it is asking for a standard dataset for msa to test a new algorithm on and the previous question is not answered as far as I can tell so it is not of much help! $\endgroup$ – Behzad Rowshanravan Jul 30 '14 at 11:33
  • $\begingroup$ @Bez: Ok. But they seems awfully linked they could be asked in single question. Anyway, I will try to answer both. $\endgroup$ – Devashish Das Jul 30 '14 at 11:39

I would suggest you PAcAlCI or Prediction of Accuracy in Alignments based on Computational Intelligence, though the acronym in wierd the tool is good for testing new Sequence Alignments. They

But before you start testing your algorithm, I suggest take a look at these papers:

[1] Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

[2] Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

PS: I haven't tested or used the tool myself.


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