Bioinformatics Genomics and DNA Analysis

Analytical and Computational Tools

  • The Broad Institute Genomic Center for Infectious Diseases
    • AVA454
      AssembleViral454 is an assembler designed for small and non-repetitive genomes sequenced at high depth.
    • HUMAnN
      The HMP Unified Metabolic Analysis Network is a pipeline for efficiently and accurately determining the presence/absence and abundance of microbial pathways in a community from metagenomic data.
    • PASA
      The Program to Assemble Spliced Alignments is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures and to maintain gene structure annotation consistent with the most recently available experimental sequence data.
    • PriSM
      A set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.
    • Prodigal
      Prokaryotic Dynamic Programming Genefinding Algorithm is a microbial (bacterial and archaeal) gene finding program.
    • QIIME
      Quantitative Insights Into Microbial Ecology is an open source software package for comparison and analysis of microbial communities.
    • RC454
      ReadClean454 is a program that takes a set of 454 read and quality files as well as a consensus assembly for those reads and corrects for known 454 error modes.
    • Trinity
      This represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
    • V-Phaser
      Use this tool to call variants in genetically heterogeneous populations from ultra-deep sequence data.
    • V-Profiler
      This tool takes a read alignment and a list of accepted variants at each location in the alignment (such as would be generated by V-Phaser) and analyzes the intra-host diversity of a genome.
    • VICUNA
      This program is a de novo assembly program targeting populations with high mutation rates.
  • NIH Center for Human Immunology, Autoimmunity and Inflammation
  • EuPathDB BLAST
  • HIV Databases
  • Immunology Database and Analysis Portal (ImmPORT)
    • Gene Pattern (iGene Pattern)
    • Linkage File Generation (PED Generation)
    • Haploview
    • MHC Sequence Feature Variant Type (SFVT) Analysis
    • Tag SNP
  • Influenza Research Database (IRD)
  • The JCVI Genomic Center for Infectious Diseases
    • AutoCloser
    • CLOE
      Software for the finishing stage, also known as closure.
    • Elvira
      A set of tools and procedures designed for high throughput assembly of small genomes such as viruses.
    • Ergatis
      A Web-based utility that is used to create, run, and monitor reusable computational analysis pipelines.
    • PANDA
      The Protein And Nucleotide Data Archive unifies the archival of the sequences from Taxonomy, GenBank, RefSeq, UniProt, PDB, and PRF on a regular interval to build and maintain a data archive.
    • PanOCT
      The Pan-genome Ortholog Clustering Tool is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains.
    • Primer Designer
      This is a high-throughput PCR primer design software.
    • SSS
      This software organizes large chunks of data.
    • Sybil
      This is is a Web-based software package for comparative genomics.
    • VIGOR
      The Viral Genome ORF Reader supports high throughput feature prediction and annotation.
    This is a Web-based software program developed for human immunoglobulin V(D)J recombination analysis.
  • jpHMM at GOBICS (jumping profile Hidden Markov Model)
    This is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family.
  • Pathogen Portal RNA-Seq Pipeline (BRC)
  • Pathosystems Resource Integration Center (PATRIC)
  • Systems Biology for Infectious Disease Research
    • CSDeconv
      Computational method to locate TF binding from ChIP-seq data using blind deconvolution.
    • GenomeView
      Genome editor and viewer with dynamic visualization of aligned short read sequences.
  • Vectorbase
  • Virus Pathogen Resource (ViPR)
    • Identify Similar Sequences (BLAST)
    • Visualize Aligned Sequences
    • Align Sequences (MSA)

Databases and Data Sets

Visualization and Modeling Tools

Clinical Genomics

Contact Information

For more information on Bioinformatics Genomics and DNA Analysis, email:
Bioinformatics and Computational Sciences Branch

Content last reviewed on December 10, 2015