CMPD: cancer mutant proteome database Release!

CMPD is designed for providing a comprehensive, integrated and well-annotated resource, focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations. The mutated protein sequence pool was based on the exome sequencing results of NCI-60 cell lines, The Cancer CellLine Encyclopedia (CCLE) and 5,600 more cases from 20 TCGA cancer genomics studies. The identified genetic alterations (SNVs and InDels) were converted to all plausible mutated protein sequences according to each altered transcript. Moreover, CMPD also provides intuitive and flexible cascade architecture to prioritize candidate targets of interest. The mutated protein seqeuneces resulted from SNVs and InDels were predicted and added to the CMPD database, which can be retrieved and used in Mass spectrometry (MS)-based seqeunce database search.

Vanno: A Visualization-aided Variant Annotation Tool Release!

Vanno integrates information from a wide variety of biomedical databases, functional predictions from currently available evaluation models and mutation landscapes from 18 TCGA cancer types. A highly integrated framework that incorporates filtering, sorting, clustering and visual analytics (e.g., Circos, Heatmap, Protein Domain, 3D structure ) modules is provided to facilitate simultaneous exploration of oncogenomics datasets at different levels such as gene, variant, protein domain or 3D structure, which is crucial for the successful extraction of knowledge from sequence alterations as well as translating biological insights into clinical applications.

ChIPseek, A website for ChIP data analysis is Release!
ChIPseek, a web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses. ChIPseek can provide statistical summary of the dataset including histogram of peak length distribution, histogram of distances to the nearest transcription start site (TSS), and pie chart (or bar chart) of genomic locations for users to have a comprehensive view on the dataset for further analysis. For examining the potential functions of peaks, ChIPseek provides peak annotation, visualization of peak genomic location, motif identification, sequence extraction, and comparison between datasets. Beyond that, ChIPseek also offers users the flexibility to filter peaks and re-analyze the filtered subset of peaks. ChIPseek supports 20 different genome assemblies for 12 model organisms including human, mouse, rat, worm, fly, frog, zebrafish, chicken, yeast, fission yeast, Arabidopsis, and rice.

Cancer Panel Analysis Pipeline (CPAP) Release!

Cancer Panel Analysis Pipeline (CPAP) is an automatic pipeline for the analysis of Ion AmpliseqTM Cancer Panel target sequencing datasets generated by the Life Technologies Ion Personal Genome Machine™(PGM™) sequencer. High throughput sequencing of cancer panel by using the bench top Ion Torrent sequencer is the most powerful application for clinical genetic testing and screening SNPs. Although the Ion Torrent sequencing machine preinstalled a Torrent Suite Software with a variant caller plugin for identifying variants from the sequencing result of each sample, no additional tools are available for the comparative analysis and visualization of multiple datasets.

FastAnnotator Release !
We present FastAnnotator, an automated annotation web tool designed to efficiently annotate sequences with their gene functions, enzyme functions or domains. FastAnnotator is useful in transcriptome studies and especially for those focusing on non-model organisms or metatranscriptomes.

VIP DB (a viral protein domain usage and distribution database.) Release!

VIP DB (a VIral Protein domain usage and distribution DataBase) is a database which associate virus protein domains with their putative biological functions and interacting partners.

DSAP (deep-sequencing small RNA analysis pipeline) Release!

DSAP is a web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA. The functions of DSAP suite include adaptor removal, clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase databases respectively.

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  1. GeneGo / MetaCore
  2. Bioinformatics Linux Cluster (BLC)
  3. Vector NTI
  4. Protein Annotation Pipeline