A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies Long Description (required)
indel-Seq-Gen (iSG) is a biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies. This is accomplished through the addition of subsequence length constraints and lineage- and site-specific evolution. iSG tracks insertion and deletion processes that occur during the simulation run. iSG records all evolutionary events and outputs the "true" multiple alignment of the sequences, and can generate a larger simulated sequence space by allowing the use of multiple related root sequences. iSG can be used to test the accuracy of multiple alignment methods, evolutionary hypotheses, ancestral protein reconstruction methods, and protein superfamily classification methods. http://bioinfolab.unl.edu/~cstrope/iSG/
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 17158778 ],
Strope CL, Scott SD, Moriyama EN ,
indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels. ,
Mol Biol Evol ,
03-01-2007 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=17158778, Primary Citation
[Pubmed ID: 32785673 ],
Aadland K, Kolaczkowski B ,
Alignment-Integrated Reconstruction of Ancestral Sequences Improves Accuracy. ,
Genome Biol Evol ,
09-01-2020 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=32785673, , Application
[Pubmed ID: 32883749 ],
Dai H, Guan Y ,
The Nubeam reference-free approach to analyze metagenomic sequencing reads. ,
Genome Res ,
09-01-2020 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=32883749, , Application