UCSC Genome Browser: Best Links

b9dc3240a346ac40fcbce3edb72213c77ca31522 kuhn Thu Dec 20 14:48:40 2012 -0800 removing bestlinks.html diff --git src/hg/htdocs/bestlinks.html src/hg/htdocs/bestlinks.html deleted file mode 100755 index 704822d..0000000 --- src/hg/htdocs/bestlinks.html +++ /dev/null @@ -1,495 +0,0 @@ - - - - - - - UCSC Genome Browser: Best Links - - - - - - - - - - -

- - -

- 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 -

- -