| | | | 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.
	
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 | | | | Main Databases |   | 
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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
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 | | | | Genome Browsers & "Complete" Genomes |   | 
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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
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 | | | | Gene Prediction and Feature Finding |   | 
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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 
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 | | | | Protein Tools and Browsers |   | 
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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
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 | | | | Family Specific |   | 
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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
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 | | | | Blast, Blat, and Align Sequences |   | 
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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
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 | | | | Tool Collections |   | 
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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
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 | | | | Journals, Alerts, and General Internet |   | 
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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
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