Bioinformatics Proteomics and Protein Analysis

Analytical and Computational Tools

• BLAST@VectorBase.org
  Bioinformatics resource for invertebrate vectors of human pathogens
• Center for Structural Genomics of Infectious Diseases
  A consortium of laboratories using state-of-the-art structural biology methods to determine the 3-D structures of proteins from pathogens in the NIAID Category A-C priority lists and organisms causing emerging and re-emerging infectious diseases.
• EuPathDB BLAST
  A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens.
• HIV Databases
  
  • ELF/Epitope Location Finder
    Search a submitted protein sequence for known epitopes from our immunology databases; epitopes predicted by consensus binding motifs; epitopes predicted by the IEDB binding algorithm.
  • ElimDupes/Duplicate Sequence Removal
    Given an alignment or set of unaligned nucleotide or protein sequences, this tool compares the sequences and eliminates any duplicates or very similar sequences, thus producing a set of unique sequences.
  • Entropy/Shannon Entropy-Two
    Compares two sets of aligned sequences (named query and background sequences) and determines if there is greater variability in one set relative to the other.
  • Gap Strip/Squeeze v 2.1.0
    Delete aligned columns that contain a chosen percentage of gaps or other characters.
  • Gene Cutter/Sequence Alignment and Protein Extraction
    A sequence alignment and protein extraction tool. It can be used for any set of nucleotide sequences for HIV-1, HIV-2 or SIV.
  • HIV Sequence Locator
    This tool finds the position of your nucleotide or protein sequence(s) relative to the appropriate viral reference strain. Or it can give you a sequence based on its coordinate location. See details below.
  • Mosaic Vaccine Tool Suite
    The three tools that make up this suite allow users to design and assess vaccine candidate protein sequences.
  • Motif Scan/HIV HLA Anchor Residue Motifs
    Find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; search any single protein for all known HLA anchor residue motifs; view motif libraries.
  • N-GlycoSite
    This tool highlights and tallies predicted N-linked glycosylation sites (Nx[ST] patterns, where x can be any amino acid).
  • PepMap
    This tool maps an input set of peptides on the HIV reference sequence HXB2.
  • QuickAlign
    Align a desired region to premade alignments or your own alignment.
  • SeqPublish/Sequence Alignment Publishing Tool
    This interface takes a sequence alignment (nucleotides or amino acids) and replaces residues identical to a reference sequence with dashes.
  • Translate/Translate Nucleotide to Amino Acid Sequences
    This tool translates nucleotide sequences and returns amino acid sequences.
  • VESPA/Viral Epidemiology Signature Pattern Analysis
    This program detects signature patterns (atypical amino acid or nucleotide residues) in a set of query sequences relative to a set of reference sequences.
• Immune Epitope Database and Analysis Resource (IEDB)
  The IEDB is cooperative research based on advanced technologies in order to efficiently translate enhanced understanding of immune function and pathophysiology to the clinic.
  • B Cell Epitope Prediction Tools
  • Epitope Conversancy Analysis
  • Epitope Sequence and 3D Structural Homology Mapping
  • T Cell Epitope Prediction Tools
• Influenza Research Database (IRD)
  
  • Identify Point Mutations
    This tool will scan the specified proteins that are from type A viruses with the specified subtype found in the IRD database for the presence of the amino acid you specify at the coordinate (location) indicated.
  • Identify Short Peptides in Influenza Proteins
    This search allows you to find short amino acid strings or oligopeptides in target proteins. It is useful for finding epitopes, ligand binding sites, or sequence domains, from among a target set of proteins.
  • Identify Similar Sequences (BLAST)
    Use BLAST algorithms to identify similar nucleotide or amino acid sequences in a variety of custom IRD databases.
  • Visualize Aligned Sequences
    Use the JalView interactive alignment viewer to visualize nucleotide or amino acid sequences provided.
• JOINSOLVER
  A Web-based software program developed for human immunoglobulin V(D)J recombination analysis.
• Pathogen Functional Genomics Resource Center (PFGRC): please note this program has ended. Software developed by the PFGRC is available at: http://www.pathogenportal.org/portal/portal/PathPort/ADB/ADB?action=a&windowstate=normal&c=pfgrcs.
  
  • APEX: Quantitative Proteomics Tool
  • Katsura: Metabolic Pathway Analysis Tool
• Pathosystems Resource Integration Center (PATRIC)
  
  • BLAST
  • Comparative Pathway Tool
    This tool allows you to identify a set of pathways based on taxonomy, EC number, pathway ID, pathway name and/or specific annotation type.
• Systems Biology for Infectious Diseases
  
  • VESPA
    Software to integrate peptide-centric proteomic data with HTP quantitiative data.
  • SIEVE
    A computational method to identify conserved protein sequences of type III secretion systems.
  • Peptide Abundance Analysis Toolbox (PAAT)
  • QC workflow for Proteomics Data: RMD
    A statistical program to determine if LC-MS peptide abundance data are statistical outliers.
• Virus Pathogen Resource (ViPR)
  
  • Align Sequences (MSA)
  • Identify Short Peptides in Proteins
  • Identify Similar Sequences (BLAST)
  • Visualize Aligned Sequences

Databases and Data Sets

• Clinical Proteomics Centers
  
  • Dengue Biomarkers
• Database of Mutations Causing Human Hyper Ige Syndrome (STAT3base)
• EuPathDB Sequence Retrieval
  Retrieve sequences by gene IDs.
• HIV Databases
  
  • Epitope Alignments
    The alignments are FASTA files of the unique epitope sequences aligned to the LANL HIV subtype reference alignments.
  • HIV Sequence Alignments
    Includes: web alignments, filtered web alignments, subtype reference alighments, compendium alignments, consensus/ancestral sequences, and RIP alignment.
  • HIV-1 Resistance Mutation Database
  • Motif Scan/HIV HLA Anchor Residue Motifs
    Find HLA anchor residue motifs within protein sequences for specified HLA genotypes, serotypes, or supertypes; search any single protein for all known HLA anchor residue motifs; view motif libraries.
• HIV-1, Human Protein Interaction Database
  The HIV-1, human protein interaction data presented here are based on literature reports.
• Immune Epitope Database and Analysis Resource (IEDB
  The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.
  • B Cell Search
  • Epitope Search
  • Identifier Search
  • MHC Ligand Elution Search
  • T Cell Search
• Immunology Database and Analysis Portal (ImmPORT)
  
  • Cell Type Ontology Browser
  • Gene Query
  • ImmPORT Gene Lists
  • Pathway Query
  • Protein Network Query
• Influenza Research Database (IRD)
  
  • 3D Protein Structures
    Search for 3D protein structure files obtained from the Protein Data Bank.
  • Immune Epitope Search
    Search for experimentally determined and predicted epitopes.
  • Nucleotide Sequence Search
    Search for influenza sequences, proteins, and strains using two types of searches.
  • Sequence Feature Variant Types (beta)
    This component provides data on specific characteristic regions and/or sub-regions termed 'Sequence Features' (SF) defined for all influenza virus proteins.
• Pathosystems Resource Integration Center (PATRIC)
  
  • Gene Ontology Finder
    The GO Search tool enables researchers to locate proteins annotated with specified GO criteria.
  • Host Pathogen Interactions
  • Protein Family Sorter Tool
  • Proteomics Resource Centers (PRC)
  • Systems Approach to Immunology/Computational Core
    Aggregates and integrates data from consortium Cores; constructs pipelines for automated data processing; disseminates consortium data to the scientific community.
• Structural Genomics Centers
  
  • Center for Structural Genomics of Infectious Diseases
    CSGID applies state-of-the-art high-throughput structural biology technologies to experimentally characterize the three dimensional atomic structure of targeted proteins from pathogens in the NIAID Category A-C priority lists and organisms causing emerging and re-emerging infectious diseases.
  • Seattle Structural Genomics Center for Infectious Disease
    SSGCID’s primary mission is to determine the structure of ca. 70 protein targets from NIAID Category A-C agents, as well as emerging and re-emerging infectious disease organisms.
• Systems Biology of Infectious Diseases
  A multi-institution center established to deepen our fundamental understanding of the complex processes of microbes and their interactions with the host.
  • Salmonella data sets
  • Yersinia Pestis data sets
  • Influenza SILAC data sets
• Influenza-host interactions
  The goal of this project is to identify the compendium of host proteins that interact directly with influenza viral proteins.
• Influenza/SARS data sets

• Virus Pathogen Resource

• ViPR Search

Visualization and Modeling Tools

• NIH Center for Human Immunology, Autoimmunity and Inflammation
  The Center mission is cooperative research based on advanced technologies in order to efficiently translate enhanced understanding of immune function and pathophysiology to the clinic.
• Highlighter (for Amino Acid Sequences)
  This tool highlights matches and mismatches in a set of aligned amino acid sequences.
• HIMMER
• HIV Databases
  
  • PeptGen Peptide Generator
    Generates sets of overlapping peptides that can be used for peptide design and epitope mapping.
  • Pixel
    This tool generates an image of an alignment using 1 or more colored pixel(s) for each residue, thus allowing errors in large alignments to be easily seen.
  • Protein Feature Accent
    View 3D structures of HIV proteins and to map a desired sequence (e.g., short functional domain or epitope) directly onto the interactive graphic.
• ImmPORT/Jmol MHC Sequencing Feature Structure Viewer
• Influenza Research Database/Visualize Aligned Sequences
  Search for 3D protein structure files obtained from the Protein Data Bank.
• PATRIC/Host Pathogen Interactions
• Visualize Aligned Sequences

Contact Information

For more information on Bioinformatics Proteomics and Protein Analysis, email:
Bioinformatics and Computational Sciences Branch

Content last reviewed on October 27, 2016