Software and Data
The CIBR Center has purchased two computational software site licenses.
The following is a continually updated table of software and data collections that are produced and distributed by CIBR Center faculty members of BCM.
|Genboree||Dr. Aleksandar Milosalvjevic||Internet-based turnkey software system for genomic research|
|PASH||Fast and accurate sequence comparison and pattern discovery in genomic sequences by parallelization|
|Spikoscope||Dr. Fabrizio Gabbiani||Browsing and analysis of electrophysiology recordings.|
|OPUS suite||Dr. Jianpeng Ma||Molecular structure modeling.|
|Evolutionary Trace Server
||Dr. Olivier Lichtarge||Ranks amino acid residues in a protein sequence by their relative evolutionary importance. Pre-computed ET analyses for select PDB IDs.|
|Report Maker||Ranks amino acid residues in a protein sequence with a UniProt accession number.|
|ET 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|
|Evolutionary Trace Code||Ranks amino acid residues in a protein sequence by their relative evolutionary importance.|
|Evolutionary Trace Annotation||The server suggests molecular functions for proteins structures based on local structural similarities to proteins of known function identified using 3D templates.|
|Contact Metric Server||Detection of similarity in protein structure and function through contact metric distances.|
|ClassA GPCRs||Difference Evolutionary Trace Server for G Protein-Coupled Class A Receptors|
|SimPed||Dr. Suzanne Leal||Generates haplotype and/or genotype data for large numbers of marker loci.|
|BSMAP||Dr. Wei Li||General-purpose bisulfite mapping software for epigenomics.|
|CEAS||An integrated webserver for analyzing ChIP-chip data.|
|DANPOS||Comparison of nucleosome maps, histone modification maps, or protein binding maps generated based on high-throughput sequencing.|
|MACS||A model-based algorithm for finding enriched regions in ChIP-Seq experiments.|
|MAT||A model-based algorithm for finding enriched regions in ChIP-Chip experiments.|
|xMAN||Rapid mapping of millions of query oligonucleotide fragments to the genome of any given length.|
|BIMBAM||Dr. Yongtao Guan||Genotype imputation and statistical tests for disease association|
|piMASS||Multi-SNP association with disease phenotypes.|
|EMAN2||Dr. Steve Ludtke||Scientific image processing suite, aimed at improving the resolution and quality of single particle reconstructions.|
|EMEN2||An extesible, object-oriented electronic lab notebook|
|Gorgon||Interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes.|
The database contains a variety of publicly accessible cryoEM single particle analysis data sets collected at NCMI.
The latest map of human genetic variation – dubbed HapMap3 – includes 11 populations from across the globe, identifying not only the single nucleotide polymorphisms (SNPs) or single letter changes in the 3 billion letter alphabet of the human genome but also 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.
A protein interaction network comprised of direct and indirect interactions of human ataxia disease-causing proteins.
Affymetrix MGU74Av2 microarray data used in identifying signatures of proliferation and quiescence in hematopoetic stem cells.