:: DESCRIPTION
mutation3D is a functional prediction and visualization tool for studying the spatial arrangement of amino acid substitutions on protein models and structures.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Heu-MCHC is a fast and accurate heuristic for the Minimum-Change Haplotype Configuration (MCHC) problem, i.e. a combinatorial formulation of the haplotype inference problem on pedigree data where the total number of recombinations and point mutations has to be minimized.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yuri Pirola, Paola Bonizzoni, and Tao Jiang.
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume: 9 , Issue: 1 Page(s): 12 – 25 (2011).
:: DESCRIPTION
ENTPRISE is an algorithm for predicting human disease-associated amino acid mutations from sequence entropy and predicted protein structures
ENTPRISE-X is an algorithm for predicting human disease-associated frameshift & nonsense mutations.
::DEVELOPER
Center for the Study of Systems Biology
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures.
Zhou H, Gao M, Skolnick J.
PLoS One. 2016 Mar 16;11(3):e0150965. doi: 10.1371/journal.pone.0150965.
Zhou H, Gao M, Skolnick J.
ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations.
PLoS One. 2018 May 3;13(5):e0196849. doi: 10.1371/journal.pone.0196849. PMID: 29723276; PMCID: PMC5933770.
:: DESCRIPTION
DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 27.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y1, Li B, Tan R, Zhu X, Wang Y.
:: DESCRIPTION
SAAMBE (Single Amino Acid Mutation related change of Binding Energy) method addresses the demand for computational tools of predicting the effect of single amino acid substitution on the binding free energy of protein complexes. It is based on the fast (<< 1 minute) modified MM-PBSA protocol that is successfully tested and optimized for more than thousand experimental data points.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.
Petukh M, Dai L, Alexov E.
Int J Mol Sci. 2016 Apr 12;17(4). pii: E547.
:: DESCRIPTION
SAAFEC-SEQ is an online application for calculating folding free energy changes in proteins caused by missense mutations for provided protein sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Li G, Panday SK, Alexov E.
SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability.
Int J Mol Sci. 2021 Jan 9;22(2):606. doi: 10.3390/ijms22020606. PMID: 33435356; PMCID: PMC7827184.
SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.
Getov I, Petukh M, Alexov E.
Int J Mol Sci. 2016 Apr 7;17(4). pii: E512. doi: 10.3390/ijms17040512.
:: DESCRIPTION
MonSTR is a tool for calling de novo mutations from HipSTR or GangSTR VCF files.)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M.
Patterns of de novo tandem repeat mutations and their role in autism.
Nature. 2021 Jan;589(7841):246-250. doi: 10.1038/s41586-020-03078-7. Epub 2021 Jan 13. PMID: 33442040; PMCID: PMC7810352.
:: DESCRIPTION
Diamund is a new, efficient algorithm for variant detection that compares DNA sequences directly to one another, without aligning them to the reference genome.
::DEVELOPER
The Center for Computational Biology at Johns Hopkins University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hum Mutat. 2014 Mar;35(3):283-8. doi: 10.1002/humu.22503.
DIAMUND: direct comparison of genomes to detect mutations.
Salzberg SL, Pertea M, Fahrner JA, Sobreira N.
:: DESCRIPTION
MEGA-V is an open-source R application with a Shiny web interface. It identifies gene sets with a significantly higher number of variants in a cohort of interest (cohort A) as compared to (1) a control cohort (cohort B) or (2) a random distribution generated using Monte Carlo.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Gambardella G, Cereda M, Benedetti L, Ciccarelli FD.
MEGA-V: detection of variant gene sets in patient cohorts.
Bioinformatics. 2017 Apr 15;33(8):1248-1249. doi: 10.1093/bioinformatics/btw809. PMID: 28003259; PMCID: PMC5408849.
:: DESCRIPTION
WExT (Weighted Exclusivity Test) is computes a statistical score for mutually exclusive mutations using per gene, per sample weights.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Leiserson MD, Reyna MA, Raphael BJ.
A weighted exact test for mutually exclusive mutations in cancer.
Bioinformatics. 2016 Sep 1;32(17):i736-i745. doi: 10.1093/bioinformatics/btw462. PMID: 27587696; PMCID: PMC5013919.
