Data Software & Data Collections (CIBR Center)

The following data software and data collections are primarily produced and distributed by CIBR Center faculty members. The sites and site content are continuously being updated and all questions related to the software and data collections should be directed to the listed faculty member.

• Genboree - Internet-based turnkey software system for genomic research.
• PASH - Fast and accurate sequence comparison and pattern discovery in genomic sequences by parallelization.

• Spikoscope - Browsing and analysis of electrophysiology recordings.

• Evolutionary Trace Server - Ranks amino acid residues in a protein sequence by their relative evolutionary importance. Pre-computed ET analyses for select PDB IDs.
• Universal Evolutionary Trace Server - Alternate option to original Evolutionary Trace Server.
• Evolutionary Trace Code - Ranks amino acid residues in a protein sequence by their relative evolutionary importance.
• Universal Evolutionary Action Server- Predicts the severity of the impact of amino acid change will have on a protein's function, given a UniProt ID or FASTA sequence.
• Evolutionary Trace Annotation - The server suggests molecular functions for protein structures based on local structural similarities to proteins of known function identified using 3D templates.
• Evolutionary Trace Viewer - Performs ET analyses starting from PDB file names or PDB formatted files.
• PyETV - An application for mapping evolutionary traces onto protein structures in PyMOL.
• Report Maker - Ranks amino acid residues in a protein sequence with a UniProt accession number.
• Contact Metric Server - Detection of similarity in protein structure and function through contact metric distances.
• Class A GPCRS - Difference Evolutionary Trace Server for G Protein-Coupled Class A Receptors.

• EMAN2 - Scientific image processing suite, aimed at improving the resolution and quality of single particle reconstructions.
• EMEN2 - An extensible, object-oriented electronic lab notebook.
• Gorgon - Interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes.

Epigenomics

• BSMAP/RRBSMAP - Whole genome (RRBS) Bisulfite Sequence MAPping program (BMC Bioinformatics 2009; Bioinformatics 2012)
• DANPOS - Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing (Genome Research 2013)
• BSeQC - Quality Control of Bisulfite Sequencing Experiments (Bioinformatics 2013)
• MOABS - MOdel based Analysis of Bisulfite Sequencing data (Genome Biology 2014)
• Mace - Model Based Analysis of ChIP-exo (Nucleic Acids Res 2014)

Transcriptomics

• RSeQC - Quality Control of RNA-seq experiments (Bioinformatics 2012)
• CPAT - Coding-Potential Assessment Tool using an alignment-free logistic regression model (Nucleic Acids Res 2013)
• DaPars - Dynamic analysis of Alternative Polyadenylation from RNA-seq (Nature 2014; Nature Communications 2015)

• hapQTL - haplotype Quantitative Loci software performs association testing between local haplotypes and phenotypes at each core marker.
• ELAI - Efficient Local Ancestry Inference software performs local ancestry inference for admixed individuals.
• piMASS - posterior inference via Model Averaging and Subset Selection software performs genome-wide joint analysis of all SNPs in association with a phenotype. Markov chain Monte Carlo is used to perform subset selection and model averaging.
• BIMBAM - Bayesian Imputation Based Association Mapping software performs genotype imputation and statistical tests for disease association, including single SNP tests and regional multi-SNP tests.

• HapMap3 - Includes 11 populations from across the globe, identifying the SNPs or single letter changes in the 3 billion letter alphabet of the human genome and variations that represent differences in the numbers of copies of genes or gene segments.

• HapMap3 - Includes 11 populations from across the globe, identifying the SNPs or single letter changes in the 3 billion letter alphabet of the human genome and variations that represent differences in the numbers of copies of genes or gene segments.

• BCM joins other institutions in characterizing the thousands of microbial species that co-exist in various parts of the human body, and shape human physiology.