UCSC Genome Bioinformatics Best Links
| This page contains links to useful databases, browsers, and tools. The collection is primarily oriented toward human and mouse genomes. To be included on this page, a tool must be web-oriented, allow free access with no registration barriers, be usable without installation or scripts, and be bioinformatic in nature. There are many internet sites that provide good, comprehensive resource lists. Google is also an excellent resource for searching for bioinformatics tools on the internet. Because of the alternative options available, this page is maintained but is no longer actively updated. The links were last validated on 29 June 05. Additions and corrections should be sent to genome-admin@soe.ucsc.edu.
Main Databases Genome Browsers and Complete Genomes Gene Prediction and Feature Finding Protein Tools and Browsers Family Specific Blast, Blat, and Align Sequences Tool Collections Journals, Alerts, and General Internet |
Main Databases |
PubMed -- abstracts for 11 million biomedical articles Entrez -- gateway to nucleotide and protein sequences LocusLink -- curated sequence and gene descriptions PDB -- 3D protein database at RCSB SwissProt -- keyword search annotated protein collection SRS -- query Swiss sequence retrieval system EBI SRS -- query session at EBI sequence retrieval center EMBL -- gateway to EMBL sequence and structure databases Hovergen -- homologous vertebrate genes database HUGE -- unidentified human proteins in KIAA series MIPS -- gateway to protein information center in Munich OWL -- non-redundant protein sequence database PIR -- gateway to PIR protein database and query tools ChromList -- lists UniGene clusters by chromosome ChromProt -- lists human proteins by chromosome KEGG -- Kyoto encyclopedia of pathways and maps Taxonomy -- taxonomic classes at NCBI TreeLife -- tree of life taxonomy project Hugo -- recommended gene symbols at Genew3 OMIM 1+ 2 -- simple and complex searches at OMIM Marshfield -- genetic and physical maps at Marshfield HGMD Mut -- human gene mutation database at Cardiff LocMutations -- locus-specific mutation databases Mitomap -- human mitochondrial genome database MitoWustl -- mitochondrial genes, mutations and disorders MitoP -- mitochondrial genes, proteins and diseases from the Mitochondria Project MitoDat -- nuclear genes specifying mitochondrial biogenesis UDB -- integrated human genome map UniGene -- query UniGene Marker -- search for marker, YACs, contigs SNP -- single nucleotide polymorphisms at SNP Consortium dbSNP -- search for single nucleotide polymorphisms at NCBI WebQTL -- QTL expression databases to explore gene interactions in recombinant inbred mice TransTerm -- sequence context of stop and start codons ESTScan -- detects coding regions despite frameshifts and low quality RegulonDB -- transcription regulation database for various organisms Rebase -- restriction enzyme cleavage sites SpliceDB -- canonical and non-canonical splice sites in mammals MemTrans -- genomic comparisons of membrane transport systems Geneimprint -- imprinted gene database Codon -- codon usage database
Genome Browsers & "Complete" Genomes |
UCSC Genome Browser -- human genome assembly and track browser at UCSC Ensembl -- human genome and disease gene browser at EBI/Sanger Map Viewer -- human genome assembly and map viewer at NCBI UCSC Table Browser -- query human genome and annotation database tables euGenes -- five species map browser and 37,049 human gene reports Download -- download human genome and install mirror VISTA -- portal for all VISTA comparative genomics tools VISTA Browser -- whole genome alignment browser (human, mouse, rat, drosophila, etc.) GenomeVISTA -- align sequences to genome assemblies (human, mouse, etc.) ECR Browser -- visualization and study of evolutionary relationships between vertebrate and non-vertebrate genomes rVista -- tool for finding potential regulatory elements in noncoding regions of the human genome TIGR CMR -- comprehensive microbial resource and genome browser NCBI -- human and animal genome projects at NCBI Sanger -- human genome project at Sanger Centre Jax -- mouse genomics at Jackson Laboratory RatMap -- rat genome database at Goteborg Zfin -- zebrafish information network and database project Exofish -- genome analysis of Tetraodon nigroviridis Flybase -- database of drosophila genomics at Indiana BDGP -- fruit fly genomics center at Berkeley WormBase -- nematode mapping, sequencing and phenotypic repository ACeDB -- genetics and genomics resource launcher SGD -- yeast genome database TAIR -- the arabidopsis information resource and tool center TIGR db -- bacterial genomes at TIGR GenTotals -- monitoring tables for genome progress
Gene Prediction and Feature Finding |
Acembly/AceView -- gene models reconstructed solely from mRNA and EST evidence Genscan D + M -- identification of complete gene structures in genomic DNA GenomeScan -- predicts genes incorporating protein homology RGD -- comparative mapping tool for rat-mouse-humany synteny FGENESH -- splice sites, coding exons, gene models, promoter and polyA Softberry -- nucleotide sequence analysis, genes, promoters TwinScan -- gene prediction for eukaryotic genomic sequences WebGene -- ten tools for analysis of protein-coding gene structure GrailEXP -- exons, genes, promoters, polyA, CpG islands at ORNL GeneWise2 -- compares protein to genomic with introns and frameshifts Genie -- finds multi-exon genes only, trained for Drosophila and other invertebrate organisms AAT -- analysis and annotation tool for finding genes HMMgene -- prediction of vertebrate and nematode genes NetGene2 -- neural network predictions of splice sites GeneMark -- gene prediction server at EBI GeneID -- gene prediction of selected signals and exons Vienna RNA -- seven RNA analysis tools Reverse Comp -- reverse complement of DNA sequence McPromoter -- finds eukaryotic RNA polymerase II transcription starts PromoterScan -- predicts promoters using homologies with Pol II promoters ORF Finder -- open reading frame finder for ORFs of cutoff size Emboss -- predict CpG islands and isochores UTR -- untranslated regions of eukaryotic mRNAs AltSplice -- database of alternate splicing in ESTs and disease genes Webcutter -- finds restriction endonuclease sites ERR_WISE -- detection of frameshift sequencing errors SEQERR -- detection of frameshift error in coding regions MutCheck -- transcription and translation effect of mutations Sift -- predicts tolerated and untolerated protein substitutions TransFac -- transcription factor database and tool collection MatInspector -- searches for transcription factor binding sites VarSplice -- collection of annotated splice variants TfScan -- scans DNA sequences for transcription factors RepeatMasker -- finds retroposons and repeats Censor -- finds repeated elements, Repbase updates, maps DotPlot -- dot plot for internal DNA sequence repeats PatternHunter -- finds approximate repeat patterns in genomic DNA REPuter -- genomic repeats of all types to 100kbp Tinoco -- suggests secondary structure in RNA or DNA RNA_align -- aligns two RNA species from secondary and tertiary structures REP -- searches proteins for internal repeats Radar -- detects and aligns protein repeats Repro -- recognizes repeats in a single protein query
Protein Tools and Browsers |
UCSC Gene Sorter -- human and other proteins, can be grouped using many criteria SwissTools -- large collection of protein tools and databases Translate -- translates DNA into 6 frames ReverseTrans 1+ 2 -- reverse-translates protein into DNA SAPS -- statistical analysis of protein sequences Emboss -- peptide information and statistics Signalp -- predicts signal peptide cleavage sites Psort -- protein sorting signals TMpred -- predicts transmembrane segments and orientation TMHMM -- predicts transmembrane helices TopPred2 -- topological prediction of membrane proteins TMAP -- predicts membrane proteins from multiple alignment PREDATOR -- secondary structure from multiple sequences SSCP -- predicts helix, strand and coil from composition Jpred -- consensus method for secondary structure prediction TOPS -- protein topology atlas and tool collection POPS -- Parameter OPtimized surfaces Interpro -- integrated resource of protein families, domains and sites Pfam -- alignments and hidden Markov models of protein domains SMART -- simple modular architecture research tool ProDom -- protein domain database ScanProsite -- scans a sequence against PROSITE ProfileScan -- scans sequence against profile databases FingerPRINTScan -- search tool for Prints motifs ppsearch -- pattern search tool for DNA or protein motifs HMMER -- profile hidden Markov models for sequence analysis SAM -- sequence alignment and modeling system by HMM BLOCKS -- aligns ungapped segments of conserved protein regions IMPALA -- blast search of BLOCKS conserved protein regions BLIMPS -- improved BLOCKS search tool Motif -- searches for motifs in query sequence FPS -- family pairwise search library of protein families SCOP -- structural classification of proteins Superfamily -- genome-wide structural classification of proteins Pratt -- search for conserved patterns in protein sequences CATH -- hierarchical classification of protein domain structures MAST -- motif alignment search tool MEME -- analyzes protein and DNA for motifs TIGRFAMs -- protein families based on hidden Markov models DALI -- coordinates of query compared to PDB database 123D -- predicts tertiary structure FSSP -- fold classification based on structure PredProt -- predicts protein structure PredictProt -- threading, secondary, solvent and transmembrane Fold -- 3D structures based on homologous sequences MaxSprout -- protein backbone and side chains from alpha coordinates CE -- finds structural alignments from PDB MSD PQS -- protein quaternary structure query form at EBI DIP -- database of interacting proteins ProtFam -- average core structures for families from structure SCWRL -- sidechain placement using a rotamer library ASC -- analytic surface calculation package ProStar -- protein potential site Sweet -- constructs 3D models of oligosaccharides from formula GlycoSuiteDB -- curated relational database of glycan structures SwissPdbView -- deep view for manipulation and analysis of PDB structures PBD Viewers -- choices of plug-ins and 3D structure viewers Kinemages -- interactive 3D protein web display RasMol -- molecular visualization resource ProtExplorer -- macromolecular viewer related to RasMol Chime -- interactive web plug-in for 3D molecular structures Morph -- downloadable protein shape morpher COMBOSA3D -- combines alignment, protein 3D, and Chime to color Boxshade -- pretty shading of multiple alignments ProtCol -- tool for coloring proteins, default is by hydrophobicity ProtExpl -- protein explorer interactive software
Family Specific |
GPCRDB -- G-protein coupled receptor database NucleaRDB -- nuclear receptors at UCSF NRR1 -- nuclear receptor resource at Georgetown HORDE -- human olfactory receptor genes ImMunoGeneTics -- vertebrate immunoglobulins (IG), T cell receptors (TR), and major histocompatibility complex (MHC) GPCR -- classifies G-protein coupled recepters Secator -- classifies any protein family (receptors, tRNA synthetases) Merops -- curated database on proteases Prion -- annotated prion-doppel gene family
Blast, Blat, and Align Sequences |
Blast -- java-free NCBI blast launch SIB Blast -- blastp and tBlastn HTGS, UniGene at EMBnet WU-Blast -- blast query against user fasta database Batch -- batch blast from Baylor Blat -- quick alignment of query to human genome assembly HumFin -- blast finished human genome chromosome Mus 1+ 2 -- blast finished mouse genome by chromosome Ensembl -- blast human genome project Sanger -- blast sequencing center chromosomes Traces -- blast against raw new genomic trace reads SSAHA -- trace server at Ensembl Hunt -- search human novel transcript cDNAs WABA -- genomic to genomic comparisons Pipmaker -- percent identity plot alignment of two genomic sequences DBA -- aligns two sequences sharing conserved blocks Alfresco -- comparative genome sequence analysis ClustalW -- aligns multiple sequences MultAlin -- aligns multiple sequences with flexible formatting Lalign -- find multiple matching subsegments in two sequences Consensus -- calculates consensus to ClustalW alginment Fasta3 -- fasta3 alignment of protein sequence SNP-Fasta3 -- alignment to HgBase SNP consortium MPsrch -- alignment tool with many parameter controls ScanPS -- multi-alignment of query protein sequence
Tool Collections |
NHGRI, EBI, NCBI -- "Genome Hub" pages NCBI -- site map to extensive services BCM -- launches numerous nucleotide and protein tools CMS -- extensive directory of tools by category ABI -- very large French tool compilation NAR -- curated tool collection at Nucleic Acid Research UCSD -- genome analysis by task area Workbench -- unified area for searching and analysis EMBL1 -- collection of database searching and tools EMBL2 -- various EMBL alignment tools UCSF1+2 collections of tool links at UCSF MDC -- bioinformatics tools at Delbruck Center EBI -- tool and utility collection at EBI SDSC -- tools at San Diego Supercomputer Center Bork -- ten tool server of Bork lab Biocatalog -- bioinformatic software collection MIA -- search agent finds macromolecular information Phylip -- tools and software for phylogenies Phylo -- provides 14 utilties for phylogenetic analysis PAML -- -- maximum likelihood of evolutionary parameters and phylogenies
Journals, Alerts, and General Internet |
PubMedJB -- journal browser allows access to current issues PubCrawler -- provides alerts to new abstracts at PubMed HighWire -- publishes online journals and provides alerts New Issues -- provides entry to 35 genomics jounals GenomeBio -- free access to post-genomics journal, pre-print server PNAS -- free access to month-old articles in PNAS JBC -- nearly free access to most cited journal Science -- high circulation general science journal Nature -- gateway to restricted spin-off journals AmJHumGen -- leading disease gene annotation journal Genomics -- genomics articles sometimes stale GenomeRes -- genomic research and methods articles Pedro -- large journal (and tool) collection OMD -- online medical dictionary Google -- best internet search site for web tools Lycos -- widely used general search tool Yahoo -- internet categories and news LangTrans -- useful for rough translations between languages