Research Guides: Bioinformatics: Genes, Proteins, & Sequence Analysis

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Quick Links

Nucleotide Sequences

NCBI Nucleotide
Collection of sequences from sources such as GenBank, RefSeq, TPA, and PDB.
Basic Local Alignment Search Tool (BLAST)
Tool for comparing gene and protein sequences and finding regions of local similarity.
Help, NCBI Handbook Tutorial
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Can help indicate possible functional and evolutionary relationships and identify members of gene families.
Open Reading Frame (ORF) Finder
Graphical analysis tool that identifies all open reading frames using the standard or alternative genetic codes.
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Includes ability to save the deduced amino acid sequences and search against them with BLAST.
Splign
Tool for computing cDNA-to-genomic or spliced sequence alignments.
Help
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Includes algorithms for identifying possible gene duplications and for recognizing introns and splice signals.
VecScreen
System for identifying segments of a nucleic acid sequence that may have vector origins and removing those segments before sequence analysis or submission.
Overview, Example Results
Viral Genotyping Tool
Program that helps identify the genotype (or subtype) of viral nucleotide sequences.
Help
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Includes predefined reference genotypes for viral pathogens such as human immunodeficiency virus 1, hepatitis C virus, hepatitis B virus (HBV), and poliovirus.
European Molecular Biology Open Software Suite (EMBOSS)
Open-source software analysis package integrating a range of tools.
Help Overview, guides & FAQ
Tutorial Includes exercises
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Includes tools for sequence analysis, including sequence alignment, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis, and more. Also has extensive programming libraries.
ImMunoGeneTics (IMGT)
Integrated databases including fully annotated sequences of immunoglobulins and T cell receptors from humans and other vertebrates.

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Also includes sequences for the human major histocompatibility complex.

Genes

NCBI Gene
Database of information about genes. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
FAQ, Quick Start beginner's how-to introduction
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Searchable by free text, partial name, chromosome, sequence accession number, and other options.
HomoloGene
Automated system for detecting homologs among the annotated genes of several completely sequenced eukaryotic genomes. Includes homology and phenotype information plus paralogs in addition to orthologs.
Help Overview, tips, FAQ, etc.
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Linked to all other Entrez databases.
Coremine Medical
Information about genes and proteins presented as "literature networks" based on instances where gene or protein names appear in articles together, providing a way to visualize possible direct or indirect connections (e.g., biological interactions).
Help
GeneCards
Concise genomic, proteomic, transcriptomic, genetic, and functional information on human genes.
Guide search guide, FAQ
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Includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, and more.
Homologous Vertebrate Genes Database (HOVERGEN)
Database of homologous vertebrate genes, including protein and associated nucleotide sequences.
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Includes ability to visualize multiple alignments and phylogenetic trees. Useful for comparative sequence analysis, phylogeny, and molecular evolution studies.
Gene Ontology (GO) Project
Searching and browsing of a controlled vocabulary for genes, gene product attributes, and biological concepts that have been annotated with GO terms across different species and databases.
Help Document & FAQ, Database Guide
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Also provides tools for accessing and processing gene product annotation data contributed by GO Consortium members.
Protein ANalysis THrough Evolutionary Relationships (PANTHER)
Classifications of proteins and their genes according to families and subfamilies, molecular function, biological processes, and pathways specifying relationships.
Help overview and tips
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Includes tools for gene expression data analysis and evolutionary analysis of coding SNPs.

Gene Expression

Gene Expression Omnibus (GEO)
Public repository of high-throughput gene expression data provided by researchers.
FAQ
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Includes tools for visualizing and exploring the data, including gene expression profiles and hierarchical cluster heat maps for relationships between genes. Includes links to other sequence, mapping, and publication database resources when possible.
Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer
"...relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations."

Protein Sequences

NCBI Protein
Collection of protein sequences from sources such as GenBank, RefSeq, TPA, SwissProt, and PDB.
Conserved Domain Database (CDD)
Collection of annotated data for identifying conserved domains in protein sequences through the use of Reverse Position Specific BLAST.
Help extensive classification
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Includes 3D-structure information and domain models imported from several source databases.
Basic Local Alignment Search Tool (BLAST)
Tool for comparing gene and protein sequences and finding regions of local similarity.
Help FAQ, guide & glossary
NCBI Handbook Tutorial
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Can help indicate possible functional and evolutionary relationships and identify members of gene families.
BLink (BLAST Link)
Tool provided as part of NCBI's Entrez Protein database that shows precalculated BLAST search results for protein sequences.
Help
Conserved Domain Architecture Retrieval Tool (CDART)
Tool for conducting searches in NCBI's Entrez Protein to find protein similarities by using domain profiles that include functional annotation.
Help
Universal Protein Resource (UniProt)
Comprehensive resource for protein sequence and annotation data.
Help
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Includes amino acid sequence, protein name or description, taxonomic data, citation information, and annotation information related to biological ontologies, classifications, and cross-references.
Expert Protein Analysis System (ExPASy) Proteomics Server
Several databases related to protein molecular biology and proteomics.
Documentation
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Includes protein sequences, protein domains and families, enzyme nomenclature, and structural protein models, as well as links to sequence analysis tools and proteomics tools.
European Molecular Biology Open Software Suite (EMBOSS)
Open-source software analysis package integrating a range of tools for sequence analysis, including sequence alignment, protein motif identification, nucleotide sequence pattern analysis, codon usage analysis, and more.
Help Overview, guides & FAQ
Tutorial Includes exercises
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Includes extensive programming libraries.
Database of Interacting Proteins (DIP)
Curated set of data about protein-protein interactions.
Help
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Includes protein name, function, subcellular localization, region involved in the interaction, dissociation constant, experimental methods used, and cross-references to other biological databases when available.
G Protein-Coupled Receptor Data Base (GPCRDB)
Database of integrated and visualized data on G protein-coupled receptors, including information on sequences, ligand binding constants, mutations, multiple sequence alignments, and homology models.
Tutorial
Protein ANalysis THrough Evolutionary Relationships (PANTHER)
Classifications of proteins and their genes according to families and subfamilies, molecular function, biological processes, and pathways specifying relationships.
Help overview and tips
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Includes tools for gene expression data analysis and evolutionary analysis of coding SNPs.