Bioinformatics
- dbNSFP: dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome.
|
If you used dbNSFP v1.x, please cite our paper 1. If you used dbNSFP v2.x, please cite our papers 1 & 2. If you used dbNSFP v3.x, please cite our papers 1 & 3. If you used dbNSFP v4.x, please cite our papers 1 & 4.
|
- dbscSNV: dbscSNV includes all potential human SNVs within splicing consensus regions (−3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site), i.e. scSNVs, related functional annotations and two ensemble prediction scores for predicting their potential of altering splicing. dbscSNV can be queried as an attached database for dbNSFP.
|
- WGSA: WGSA is an annotation pipeline for human genome re-sequencing studies, to facilitate the functional annotation step of whole genome sequencing (WGS). Currently WGSA supports the annotation of SNVs and indels locally without remote database requests, allowing it to scale up for large WGS studies.
|
- dbMTS: the database for miRNA target site (MTS) SNVs, which includes all potential MTS SNVs in the 3’UTR of human genome along with hundreds of functional annotations. This database can help studies easily identify putative SNVs that affect miRNA targeting and facilitate the prioritization of their functional importance. dbMTS can be queried as an attached database for dbNSFP.
|
- MetaRNN: a deep learning based ensemble pathogenicity prediction score for nsSNVs and non-frameshift indels. MetaRNN used a recurrent neural network (RNN) to integrate information from 16 high-level pathogenicity prediction scores, 8 conservation scores, and allele frequency information from the 1000 Genomes Project (1000GP), ExAC, and gnomAD.
|
Population Genetics
- SRV: srv is a forward simulation algorithm, which simulates DNA sequences assuming realistic models for human demographic and natural selection.
|
- jPopGen Suite: jPopGen Suite is an user-friendly package of java programs for population genetic analysis of SNP spectrum data from randomly sampled DNA sequences.
|
- Stairway Plot: The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data. It does not need a pre-defined population model and can be applied to hundreds of unphased sequences.
|
If you used Stairway Plot version 0.1-1.0, please cite 1. If you used Stairway Plot version 1.5, please cite 1 & 2. If you used Stairway Plot version 2, please cite 1 & 3.
|
Office3720 Spectrum Boulevard, Suite 304
Tampa, FL 33612 |
Telephone813-974-9865
|
xiaomingliu@usf.edu
|