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 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> -<HTML> -<HEAD> - <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> - <META name="UCSC Genome Browser Links" content="UCSC Genome Browser"> - <META name="keywords" content="genome, genome browser, genome assembly, Blat, UCSC, bioinformatics, tools, gene prediction, SNP, EST, mRNA"> - <TITLE>UCSC Genome Browser: Best Links</TITLE> - <LINK REL="STYLESHEET" HREF="style/HGStyle.css"> -</HEAD> -<BODY BGCOLOR="FFF9D2" LINK="0000CC" VLINK="#330066" ALINK="#330066"> -<A NAME="TOP"></A> - - -<TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"><TR><TH COLSPAN=2 ALIGN="left"><IMG SRC="images/title.jpg" ALT="UCSC Genome Bioinformatics"></TH></TR> - -<TR><TD COLSPAN=2 HEIGHT=40><!--#include virtual="inc/topbar.html"--></TD></TR> -<!--Content Tables-------------------------------------------------------> -<TR><TD COLSPAN=2 CELLPADDING=10> -<!--outer table is for border purposes--> -<A NAME="000"></A> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <FONT SIZE="4"><B> UCSC Genome Bioinformatics Best Links </B></FONT> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH=100% CELLPADDING=0 BORDER=0><TH HEIGHT=10></TH><TR><TD WIDTH=3></TD><TD> - 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. - <P> - There are many internet sites - that provide good, comprehensive resource lists. - <A HREF="http://www.google.com" TARGET=_blank>Google</A> 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 - <A HREF="mailto:genome-admin@soe.ucsc.edu">genome-admin@soe.ucsc.edu</A>. - <!-- above address is genome-admin at soe.ucsc.edu --> - - </TD></TR><TR><TD COLSPAN=2> - <TABLE CELLPADDING=0><TH HEIGHT=5></TH><TR><TD><UL><B> - <LI><A CLASS="toc" HREF="#111"> Main Databases </A></LI> - <LI><A CLASS="toc" HREF="#122"> Genome Browsers and Complete Genomes </A></LI> - <LI><A CLASS="toc" HREF="#133"> Gene Prediction and Feature Finding</A></LI> - <LI><A CLASS="toc" HREF="#144"> Protein Tools and Browsers </A></LI> - <LI><A CLASS="toc" HREF="#155"> Family Specific </A></LI> - <LI><A CLASS="toc" HREF="#166"> Blast, Blat, and Align Sequences </A></LI> - <LI><A CLASS="toc" HREF="#177"> Tool Collections </A></LI> - <LI><A CLASS="toc" HREF="#188"> Journals, Alerts, and General Internet </A></LI> - </TD><TD VALIGN="top"></B></UL> - </TD></TR></TABLE> - </TD></TR></TABLE> - <BR></TD></TR></TABLE> -</TD></TR></TABLE> - - -<a name="111"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Main Databases</b></FONT></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?CMD=Limits&DB=PubMed">PubMed</a> -- abstracts for 11 million biomedical articles -<li><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide">Entrez</a> -- gateway to nucleotide and protein sequences -<li><a href="http://www.ncbi.nlm.nih.gov/LocusLink/">LocusLink</A> -- curated sequence and gene descriptions -<li><a href="http://www.rcsb.org/">PDB</A> -- 3D protein database at RCSB -<li><a href="http://www.expasy.ch/cgi-bin/sprot-search-ful">SwissProt</A> -- keyword search annotated protein collection -<li><A HREF="http://www.expasy.org/srs5/">SRS</A> -- query Swiss sequence retrieval system -<li><A HREF="http://srs6.ebi.ac.uk/">EBI SRS</A> -- query session at EBI sequence retrieval center -<li><a href="http://www.ebi.ac.uk/Databases/index.html">EMBL</A> -- gateway to EMBL sequence and structure databases -<li><a href="http://pbil.univ-lyon1.fr/databases/hovergen.html">Hovergen</A> -- homologous vertebrate genes database -<li><A HREF="http://zearth.kazusa.or.jp/huge/">HUGE</A> -- unidentified human proteins in KIAA series -<li><A HREF="http://srs-mips.gsf.de/">MIPS</A> -- gateway to protein information center in Munich -<li><A HREF="http://www.bioinf.man.ac.uk/dbbrowser/OWL/">OWL</A> -- non-redundant protein sequence database -<li><A HREF="http://www-nbrf.georgetown.edu/pir/searchdb.html">PIR</A> -- gateway to PIR protein database and query tools -<li><A HREF="http://www.ncbi.nlm.nih.gov/UniGene/query_tips.html">ChromList</A> -- lists UniGene clusters by chromosome -<li><A HREF="http://www.expasy.org/cgi-bin/lists?humchr12.txt">ChromProt</A> -- lists human proteins by chromosome -<li><A HREF="http://www.genome.ad.jp/kegg/kegg3.html">KEGG</A> -- Kyoto encyclopedia of pathways and maps -<li><A HREF="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html">Taxonomy</A> -- taxonomic classes at NCBI -<li><A HREF="http://tolweb.org/tree/phylogeny.html">TreeLife</A> -- tree of life taxonomy project -<br><br> -<li><a href="http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl">Hugo</A> -- recommended gene symbols at Genew3 -<li><a href="http://www3.ncbi.nlm.nih.gov/omim/">OMIM 1</A>+ - <A HREF="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?CMD=Limits&DB=OMIM">2</A> -- simple and complex searches at OMIM -<li><a href="http://research.marshfieldclinic.org/genetics/">Marshfield</A> -- genetic and physical maps at Marshfield -<li><a href="http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html">HGMD Mut</A> -- human gene mutation database at Cardiff -<li><A HREF="http://www.ncbi.nlm.nih.gov:80/entrez/Omim/allresources.html#LocusSpecific">LocMutations</A> -- locus-specific mutation databases -<li><A HREF="http://www.mitomap.org">Mitomap</A> -- human mitochondrial genome database -<!-- -<li><A HREF="http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/mzorder?tax=40674&name=Mammalia">Mito</A> -- mitochondrial genomes and alignment ---> -<li><A HREF="http://www.neuro.wustl.edu/neuromuscular/mitosyn.html">MitoWustl</A> -- mitochondrial genes, mutations and disorders -<li><A HREF="http://www.dhgp.de/research/projects/abstracts/9605.html">MitoP</A> -- mitochondrial genes, proteins and diseases from the Mitochondria Project -<li><A HREF="http://www-lecb.ncifcrf.gov/mitoDat/">MitoDat</A> -- nuclear genes specifying mitochondrial biogenesis -<br><br> -<li><a href="http://bioinfo.weizmann.ac.il/udb">UDB</A> -- integrated human genome map -<li><A HREF="http://www.ncbi.nlm.nih.gov/UniGene/query_tips.html">UniGene</A> -- query UniGene -<!-- -<li><a href="http://www.ncbi.nlm.nih.gov/genome/seq/chr.cgi?CHR=20&SRT=ppos&MIN=0&ORG=Hs">Contigs</A> -- search NT contigs, dbSTS, GenMap99 ---> -<li><a href="http://www-genome.wi.mit.edu/cgi-bin/contig/phys_map">Marker</A> -- search for marker, YACs, contigs -<li><A HREF="http://snp.cshl.org">SNP</A> -- single nucleotide polymorphisms at SNP Consortium -<li><A HREF="http://www.ncbi.nlm.nih.gov/SNP">dbSNP</A> -- search for single nucleotide polymorphisms at NCBI -<li><a href="http://headmaster.utmem.edu/search.html">WebQTL</a> -- QTL expression databases to explore gene interactions in recombinant inbred mice -<br><br> -<li><a href="http://uther.otago.ac.nz/Transterm.html">TransTerm</A> -- sequence context of stop and start codons -<li><a href="http://www.ch.embnet.org/software/ESTScan.html">ESTScan</A> -- detects coding regions despite frameshifts and low quality -<li><a href="http://www.cifn.unam.mx/Computational_Genomics/regulondb/">RegulonDB</A> -- transcription regulation database for various organisms -<li><A HREF="http://rebase.neb.com/rebase/rebase.html">Rebase</A> -- restriction enzyme cleavage sites -<li><A HREF="http://genomic.sanger.ac.uk/spldb/SpliceDB.html">SpliceDB</A> -- canonical and non-canonical splice sites in mammals -<li><a href="http://www.biology.ucsd.edu/~ipaulsen/transport/">MemTrans</A> -- genomic comparisons of membrane transport systems -<li><a href="http://www.Geneimprint.com">Geneimprint</A> -- imprinted gene database -<li><a href="http://www.kazusa.or.jp/codon/">Codon</A> -- codon usage database -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="122"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Genome Browsers & "Complete" Genomes </b></FONT></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="index.html">UCSC Genome Browser</A> -- human genome assembly and track browser at UCSC -<li><a href="http://www.ensembl.org/perl/mapview?chr=20">Ensembl</A> -- human genome and disease gene browser at EBI/Sanger -<li><A HREF="http://www.ncbi.nlm.nih.gov/mapview/">Map Viewer</A> -- human genome assembly and map viewer at NCBI -<li><A HREF="../cgi-bin/hgText">UCSC Table -Browser</A> -- query human genome and annotation database tables -<li><A HREF="http://iubio.bio.indiana.edu:8089/man/">euGenes</A> -- five species map browser and 37,049 human gene reports -<li><A HREF="http://hgdownload.cse.ucsc.edu/downloads.html">Download</A> -- download human genome and install mirror -<li><A HREF="http://www-gsd.lbl.gov/vista">VISTA</A> -- portal for all VISTA comparative genomics tools -<li><A HREF="http://pipeline.lbl.gov">VISTA Browser</A> -- whole genome alignment browser (human, mouse, rat, drosophila, etc.) -<li><A HREF="http://pipeline.lbl.gov/cgi-bin/GenomeVista">GenomeVISTA</A> -- align sequences to genome assemblies (human, mouse, etc.) -<li><a href="http://ecrbrowser.dcode.org/">ECR Browser</A> -- visualization -and study of evolutionary relationships between vertebrate and non-vertebrate -genomes -<li><A HREF="http://rvista.dcode.org/" TARGET=_blank>rVista</A> -- tool for -finding potential regulatory elements in noncoding regions of the human -genome -<li><A HREF="http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl">TIGR CMR</A> -- comprehensive microbial resource and genome browser -<br><br> -<li><a href="http://www.ncbi.nlm.nih.gov/Genomes/index.html">NCBI</A> -- human and animal genome projects at NCBI -<li><a href="http://www.sanger.ac.uk/HGP/links.shtml">Sanger</A> -- human genome project at Sanger Centre -<li><a href="http://www.informatics.jax.org/">Jax</A> -- mouse genomics at Jackson Laboratory -<li><A HREF="http://ratmap.gen.gu.se/">RatMap</A> -- rat genome database at Goteborg -<li><a href="http://zfish.uoregon.edu/">Zfin</A> -- zebrafish information network and database project -<li><a href="http://www.genoscope.cns.fr/externe/tetraodon/">Exofish</A> -- genome analysis of Tetraodon nigroviridis -<li><a href="http://flybase.bio.indiana.edu/">Flybase</A> -- database of drosophila genomics at Indiana -<li><A HREF="http://www.fruitfly.org">BDGP</A> -- fruit fly genomics center at Berkeley -<li><A HREF="http://www.wormbase.org/">WormBase</A> -- nematode mapping, sequencing and phenotypic repository -<li><a href="http://elegans.swmed.edu/genome.shtml">ACeDB</A> -- genetics and genomics resource launcher -<li><a href="http://genome-www.stanford.edu/Saccharomyces/">SGD</A> -- yeast genome database -<li><A HREF="http://arabidopsis.org">TAIR</A> -- the arabidopsis information resource and tool center -<li><a href="http://www.tigr.org/tdb/mdb/mdbcomplete.html">TIGR db</A> -- bacterial genomes at TIGR -<li><a href="http://www.ebi.ac.uk/genomes/mot/">GenTotals</A> -- monitoring tables for genome progress -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="133"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Gene Prediction and Feature Finding </b></FONT></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD> -<UL> -<li><a href="http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html">Acembly/AceView</A> --- gene models reconstructed solely from mRNA and EST evidence -<li><a href="http://genome.dkfz-heidelberg.de/cgi-bin/GENSCAN/genscan.cgi">Genscan D</A> + - <a href="http://genes.mit.edu/GENSCAN.html">M</A> -- identification of complete gene structures in genomic DNA -<li><A HREF="http://genes.mit.edu/genomescan.html">GenomeScan</A> -- predicts genes incorporating protein homology -<li><A HREF="http://rgd.mcw.edu/">RGD</A> -- comparative mapping tool for rat-mouse-humany synteny -<li><a href="http://genomic.sanger.ac.uk/gf/gf.shtml">FGENESH</a> -- splice sites, coding exons, gene models, promoter and polyA -<li><a href="http://www.softberry.com/berry.phtml">Softberry</A> -- nucleotide sequence analysis, genes, promoters -<li><A HREF="http://genes.cs.wustl.edu/">TwinScan</A> -- gene prediction for eukaryotic genomic sequences -<li><A HREF="http://www.itba.mi.cnr.it/webgene/">WebGene</A> -- ten tools for analysis of protein-coding gene structure -<li><A HREF="http://grail.lsd.ornl.gov/grailexp/">GrailEXP</A> -- exons, genes, promoters, polyA, CpG islands at ORNL -<li><A HREF="http://www.sanger.ac.uk/Software/Wise2/genewiseform.shtml">GeneWise2</A> -- compares protein to genomic with introns and frameshifts -<li><A HREF="http://www.fruitfly.org/seq_tools/genie.html">Genie</A> -- finds -multi-exon genes only, trained for Drosophila and other invertebrate organisms -<li><A HREF="http://genome.cs.mtu.edu/aat.html">AAT</A> -- analysis and annotation tool for finding genes -<li><a href="http://www.cbs.dtu.dk/services/HMMgene/">HMMgene</a> -- prediction of vertebrate and nematode genes -<li><a href="http://www.cbs.dtu.dk/services/NetGene2/">NetGene2</a> -- neural network predictions of splice sites -<br><br> -<li><A HREF="http://www.ebi.ac.uk/genemark/">GeneMark</A> -- gene prediction server at EBI -<li><a href="http://www1.imim.es/geneid.html">GeneID</a> -- gene prediction of selected signals and exons -<li><a href="http://www.tbi.univie.ac.at/~ivo/RNA/">Vienna RNA</A> -- seven RNA analysis tools -<br><br> -<li> <a href="http://searchlauncher.bcm.tmc.edu/seq-util/seq-util.html">Reverse Comp</A> -- reverse complement of DNA sequence -<li> <A HREF="http://genes.mit.edu/McPromoter.html">McPromoter</A> -- finds eukaryotic RNA polymerase II transcription starts -<li> <A HREF="http://bimas.dcrt.nih.gov/molbio/proscan/index.html">PromoterScan</A> -- predicts promoters using homologies with Pol II promoters -<li> <A HREF="http://www.ncbi.nlm.nih.gov/gorf/gorf.html">ORF Finder</A> -- open reading frame finder for ORFs of cutoff size -<li> <A HREF="http://www.ebi.ac.uk/emboss/cpgplot/">Emboss</A> -- predict CpG islands and isochores -<li> <A HREF="http://bighost.area.ba.cnr.it/BIG/UTRHome/">UTR</A> -- untranslated regions of eukaryotic mRNAs - -<li> <A HREF="http://www.ebi.ac.uk/asd/altsplice/" TARGET=_blank>AltSplice</A> -- database of alternate splicing in ESTs and disease genes -<li> <a href="http://www.firstmarket.com/firstmarket/cutter/cut2.html">Webcutter</A> -- finds restriction endonuclease sites -<! li> <! A HREF="http://ir2lcb.cnrs-mrs.fr/d_fsed/fsed.html" FSED</A -- frameshift error detection in new sequences dead 12-02-03> -<li> <A HREF="http://www.bork.embl-heidelberg.de/ERR_WISE/">ERR_WISE</A> -- detection of frameshift sequencing errors -<li> <A HREF="http://www.bork.embl-heidelberg.de/SEQERR/">SEQERR</A> -- detection of frameshift error in coding regions -<li> <A HREF="http://www.ebi.ac.uk/cgi-bin/mutations/check.cgi">MutCheck</A> -- transcription and translation effect of mutations -<li> <a href="http://blocks.fhcrc.org/~pauline/SIFT.html">Sift</A> -- predicts tolerated and untolerated protein substitutions -<br><br> -<li> <a href="http://www.gene-regulation.com/">TransFac</A> -- transcription factor database and tool collection -<li> <A HREF="http://www.gene-regulation.com">MatInspector</A> -- searches for transcription factor binding sites -<li> <A HREF="http://www.bioinf.mdc-berlin.de/splice/">VarSplice</A> -- collection of annotated splice variants -<li> <A HREF="http://bioweb.pasteur.fr/seqanal/interfaces/tfscan.html">TfScan</A> -- scans DNA sequences for transcription factors -<br><br> -<li> <a href="http://ftp.genome.washington.edu/cgi-bin/RepeatMasker">RepeatMasker</A> -- finds retroposons and repeats -<li> <a href="http://www.girinst.org/Censor_Server-Data_Entry_Forms.html">Censor</A> -- finds repeated elements, Repbase updates, maps -<li> <a href="http://www.biophys.uni-duesseldorf.de/local/DOTPLOT/dotplot.html">DotPlot</A> -- dot plot for internal DNA sequence repeats -<li> <a href="http://www.bioinformaticssolutions.com/products/ph.php">PatternHunter</A> -- finds approximate repeat patterns in genomic DNA -<li> <a href="http://bibiserv.techfak.uni-bielefeld.de/cgi-bin/reputer_submit?mode=STARTUP">REPuter</A> - -- genomic repeats of all types to 100kbp -<li> <a href="http://www.biophys.uni-duesseldorf.de/local/TINOCO/tinoco.html">Tinoco</A> -- suggests secondary structure in RNA or DNA -<li> <a href="http://www.csd.uwo.ca/~kzhang/rna/rna_align.html">RNA_align</A> - -- aligns two RNA species from secondary and tertiary structures -<li> <A HREF="http://www.embl-heidelberg.de/~andrade/papers/rep/search.html">REP</A> -- searches proteins for internal repeats -<li> <A HREF="http://www.ebi.ac.uk/Radar/">Radar</A> -- detects and aligns protein repeats -<li> <A HREF="http://ibivu.cs.vu.nl/programs/reprowww/">Repro</A> -- recognizes repeats in a single protein query -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="144"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Protein Tools and Browsers </b></FONT></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="../cgi-bin/hgNear/">UCSC Gene Sorter</A> -- human and other proteins, can be grouped using many criteria -<li><a href="http://www.expasy.ch/tools/">SwissTools</A> -- large collection of protein tools and databases -<li><a href="http://www.expasy.ch/tools/dna.html">Translate</A> -- translates DNA into 6 frames -<li><a href="http://www.ebi.ac.uk/cgi-bin/mutations/revtransl.cgi">ReverseTrans 1</A>+ - <a href="http://www.entelechon.com/eng/backtranslation.html">2</A> -- reverse-translates protein into DNA -<li><a href="http://www.ebi.ac.uk/saps/">SAPS</A> -- statistical analysis of protein sequences -<li><a href="http://www.ebi.ac.uk/emboss/pepinfo/">Emboss</A> -- peptide information and statistics -<br><br> -<li><a href="http://www.cbs.dtu.dk/services/SignalP/">Signalp</A> -- predicts signal peptide cleavage sites -<li><a href="http://psort.nibb.ac.jp/form.html">Psort</A> -- protein sorting signals -<li><a href="http://www.ch.embnet.org/software/TMPRED_form.html">TMpred</A> -- predicts transmembrane segments and orientation -<li><a href="http://www.cbs.dtu.dk/services/TMHMM/">TMHMM</A> -- predicts transmembrane helices -<li><a href="http://www.sbc.su.se/~erikw/toppred2/">TopPred2</A> -- topological prediction of membrane proteins -<li><a href="http://www.mbb.ki.se/tmap/index.html"> TMAP</A> -- predicts membrane proteins from multiple alignment -<li><a -href="http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_predator.html">PREDATOR</A> -- secondary structure from multiple sequences -<li><a href="http://www.bork.embl-heidelberg.de/SSCP/">SSCP</A> -- predicts helix, strand and coil from composition -<li><a href="http://www.compbio.dundee.ac.uk/~www-jpred/">Jpred</A> -- consensus method for secondary structure prediction -<li><a href="http://www3.ebi.ac.uk/tops">TOPS</A> -- protein topology atlas and tool collection -<li> <A HREF="http://mathbio.nimr.mrc.ac.uk/tools/pops/">POPS</A> -- Parameter OPtimized surfaces -<br><br> -<li><a href="http://www.ebi.ac.uk/interpro/">Interpro</A> -- integrated resource of protein families, domains and sites -<li><a href="http://www.sanger.ac.uk/Pfam/">Pfam</A> -- alignments and hidden Markov models of protein domains -<li><a href="http://smart.embl-heidelberg.de/">SMART</A> -- simple modular architecture research tool -<li><a href="http://protein.toulouse.inra.fr/prodom.html">ProDom</A> -- protein domain database -<li><a href="http://us.expasy.org/tools/scanprosite/">ScanProsite</A> -- scans a sequence against PROSITE -<li><a href="http://hits.isb-sib.ch/cgi-bin/PFSCAN">ProfileScan</A> -- scans sequence against profile databases -<li><a href="http://www.ebi.ac.uk/printsscan/">FingerPRINTScan</A> -- search tool for Prints motifs -<li><a href="http://www.ebi.ac.uk/ppsearch/">ppsearch</A> -- pattern search tool for DNA or protein motifs -<li><a href="http://hmmer.wustl.edu/">HMMER</A> -- profile hidden Markov models for sequence analysis -<li><a href="http://www.cse.ucsc.edu/research/compbio/sam.html">SAM</A> -- sequence alignment and modeling system by HMM -<li><a href="http://blocks.fhcrc.org/">BLOCKS</A> -- aligns ungapped segments of conserved protein regions -<li><a href="http://blocks.fhcrc.org/blocks/impala.html">IMPALA</A> -- blast search of BLOCKS conserved protein regions -<li><a href="http://bioweb.pasteur.fr/seqanal/motif/blimps-uk.html">BLIMPS</A> -- improved BLOCKS search tool -<li><a href="http://motif.genome.ad.jp/">Motif</A> -- searches for motifs in query sequence -<li><a href="http://fps.sdsc.edu/">FPS</A> -- family pairwise search library of protein families -<li><a href="http://scop.mrc-lmb.cam.ac.uk/scop/">SCOP</A> -- structural classification of proteins -<li><a href="http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/index.html">Superfamily</A> -- genome-wide structural classification of proteins -<li><a href="http://www.ebi.ac.uk/pratt/">Pratt</A> -- search for conserved patterns in protein sequences -<li><a href="http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html">CATH</A> -- hierarchical classification of protein domain structures -<li><a href="http://meme.sdsc.edu/meme/website/mast.html">MAST</A> -- motif alignment search tool -<li><a href="http://meme.sdsc.edu/meme/website/meme.html">MEME</A> -- analyzes protein and DNA for motifs -<li><a href="http://www.tigr.org/TIGRFAMs/">TIGRFAMs</A> -- protein families based on hidden Markov models -<br><br> -<li><a href="http://www.ebi.ac.uk/dali">DALI</A> -- coordinates of query compared to PDB database -<li><a href="http://genomic.sanger.ac.uk/123D/run123D.shtml">123D</A> -- predicts tertiary structure -<li><a href="http://www.ebi.ac.uk/dali/fssp">FSSP</A> -- fold classification based on structure -<li><a href="http://www.embl-heidelberg.de/predictprotein/predictprotein.html">PredProt</A> -- predicts protein structure -<li><a href="http://cubic.bioc.columbia.edu/predictprotein/">PredictProt</A> -- threading, secondary, solvent and transmembrane -<li><a href="http://dove.embl-heidelberg.de/3D/">Fold</A> -- 3D structures based on homologous sequences -<li><a href="http://www.ebi.ac.uk/dali/maxsprout/">MaxSprout</A> -- protein backbone and side chains from alpha coordinates -<li><a href="http://cl.sdsc.edu/ce/all-to-all/all-to-all-r.html">CE</A> -- finds structural alignments from PDB -<br><br> -<li><a href="http://pqs.ebi.ac.uk/">MSD PQS</A> -- protein quaternary structure query form at EBI -<li><a href="http://dip.doe-mbi.ucla.edu/dip/Search.cgi">DIP</A> -- database of interacting proteins -<br><br> -<li><a href="http://www-camis.stanford.edu/projects/helix/LPFC/">ProtFam</A> -- average core structures for families from structure -<li><a href="http://www.fccc.edu/research/labs/dunbrack/scwrl/">SCWRL</A> -- sidechain placement using a rotamer library -<li><a href="http://www.bork.embl-heidelberg.de/ASC/">ASC</A> -- analytic surface calculation package -<!-- -<li><a href="http://promoter.ics.uci.edu/BRNN-PRED/">AA Contacts</A> -- residue contacts, solvent accessibility ---> -<li><a href="http://prostar.carb.nist.gov/">ProStar</A> -- protein potential site -<br><br> -<li><a href="http://www.dkfz-heidelberg.de/spec/sweet2/doc/">Sweet</A> -- constructs 3D models of oligosaccharides from formula -<li><a href="http://www.glycosuite.com">GlycoSuiteDB</A> -- curated relational database of glycan structures -<br><br> -<li><a href="http://www.expasy.ch/spdbv/">SwissPdbView</A> -- deep view for manipulation and analysis of PDB structures -<li><a href="http://www.rcsb.org/pdb/cgi/explore.cgi?job=graphics&pdbId=4HHB&page=&pid=11682995474077">PBD Viewers</A> -- choices of plug-ins and 3D structure viewers -<li><a href="http://www.proteinsociety.org/kinemages/kinpage.html">Kinemages</A> -- interactive 3D protein web display -<li><a href="http://www.umass.edu/microbio/rasmol/index2.htm">RasMol</A> -- molecular visualization resource -<li><a href="http://www.umass.edu/microbio/rasmol/">ProtExplorer</A> -- macromolecular viewer related to RasMol -<li><a href="http://www.umass.edu/microbio/chime">Chime</A> -- interactive web plug-in for 3D molecular structures -<li><a href="http://www.umass.edu/microbio/chime/morpher/">Morph</A> -- downloadable protein shape morpher -<li><a href="http://bioinformatics.org/combosa3d/index_b.html">COMBOSA3D</A> -- combines alignment, protein 3D, and Chime to color -<li><a href="http://www.ch.embnet.org/software/BOX_form.html">Boxshade</A> -- pretty shading of multiple alignments -<li><a href="http://www2.ebi.ac.uk/cgi-bin/translate/visprot.pl">ProtCol</A> -- tool for coloring proteins, default is by hydrophobicity -<li><a href="http://proteinexplorer.org/">ProtExpl</A> -- protein explorer interactive software - </UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - - -<a name="155"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Family Specific </b></FONT></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="http://www.gpcr.org/7tm/">GPCRDB</A> -- G-protein coupled receptor database -<li><a href="http://www.receptors.org/NR/">NucleaRDB</A> -- nuclear receptors at UCSF -<li><a href="http://biochem1.basic-sci.georgetown.edu/nrr/NRR1.html">NRR1</A> -- nuclear receptor resource at Georgetown -<li><a href="http://bioinformatics.weizmann.ac.il/HORDE/">HORDE</A> -- human olfactory receptor genes -<li><a href="http://imgt.cines.fr">ImMunoGeneTics</A> -- vertebrate immunoglobulins (IG), T cell receptors (TR), and major histocompatibility complex (MHC) -<li><a href="http://www.cse.ucsc.edu/research/compbio/gpcr-subclass">GPCR</A> -- classifies G-protein coupled recepters -<li><a href="http://www-bio3d-igbmc.u-strasbg.fr/~wicker/Secator/secator.html">Secator</A> -- classifies any protein family (receptors, tRNA synthetases) -<li><a href="http://merops.sanger.ac.uk/" TARGET=_blank>Merops</A> -- curated database on proteases -<li><a href="http://www.mad-cow.org/00/sci_archive_frame.html">Prion</A> -- annotated prion-doppel gene family -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="166"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Blast, Blat, and Align Sequences </FONT></b></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="http://www.ncbi.nlm.nih.gov/blast/index.nojs.cgi">Blast</A> -- java-free NCBI blast launch -<li><a href="http://www.expasy.org/cgi-bin/BLASTEMBnet-CH.pl">SIB Blast</A> -- blastp and tBlastn HTGS, UniGene at EMBnet -<!-- -<li><a href="http://www.ncbi.nlm.nih.gov/gorf/bl2.html">Blast2</A> -- restricts blast to user query and target ---> -<li><a href="http://www.proweb.org/proweb/Tools/WU-blast.html">WU-Blast</A> -- blast query against user fasta database -<li><a href="http://searchlauncher.bcm.tmc.edu/downloads/software/batch_client.html">Batch</A> -- batch blast from Baylor -<br><br> -<li><a href="../cgi-bin/hgBlat?command=start">Blat</A> -- quick alignment of query to human genome assembly -<li><a href="http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=HsBlast.html&&ORG=Hs">HumFin</A> -- blast finished human genome -chromosome -<li><a href="http://mouse.ensembl.org/">Mus 1</A>+ - <a href="http://www.ncbi.nlm.nih.gov/genome/seq/page.cgi?F=MmBlast.html&&ORG=Mm">2</A> - -- blast finished mouse genome by chromosome -<li><a href="http://www.ensembl.org/perl/blastview">Ensembl</A> -- blast human genome project -<li><a href="http://www.sanger.ac.uk/DataSearch">Sanger</A> -- blast sequencing center chromosomes -<li><a href="http://www.ncbi.nlm.nih.gov/blast/mmtrace.html">Traces</A> -- blast against raw new genomic trace reads -<li><a href="http://trace.ensembl.org/perl/ssahaview">SSAHA</A> -- trace server at Ensembl -<li><a href="http://www.hri.co.jp/HUNT">Hunt</A> -- search human novel transcript cDNAs -<br><br> -<li><a href="http://www.cse.ucsc.edu/~kent/xenoAli/xenAliTwo.html">WABA</A> -- genomic to genomic comparisons -<li><a href="http://bio.cse.psu.edu/pipmaker/">Pipmaker</A> -- percent identity plot alignment of two genomic sequences -<li><a href="http://www.sanger.ac.uk/Software/Wise2/dbaform.shtml">DBA</A> -- aligns two sequences sharing conserved blocks -<li><a href="http://www.sanger.ac.uk/Software/Alfresco/">Alfresco</A> -- comparative genome sequence analysis -<br><br> -<li><a href="http://www2.ebi.ac.uk/clustalw/">ClustalW</A> -- aligns multiple sequences -<li><a href="http://www.toulouse.inra.fr/multalin.html">MultAlin</A> -- aligns multiple sequences with flexible formatting -<li><a href="http://www.ch.embnet.org/software/LALIGN_form.html">Lalign</A> -- find multiple matching subsegments in two sequences -<li><a href="http://www.bork.embl-heidelberg.de/Alignment/consensus.html">Consensus</A> -- calculates consensus to ClustalW alginment -<li><a href="http://www.ebi.ac.uk/fasta33/">Fasta3</A> -- fasta3 alignment of protein sequence -<li><a href="http://www.ebi.ac.uk/snpfasta3/">SNP-Fasta3</A> -- alignment to HgBase SNP consortium -<li><a href="http://www.ebi.ac.uk/MPsrch/">MPsrch</A> -- alignment tool with many parameter controls -<li><a href="http://www.ebi.ac.uk/scanps/">ScanPS</A> -- multi-alignment of query protein sequence -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="177"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Tool Collections </FONT></b></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="http://www.genome.gov/">NHGRI</A>, - <a href="http://www.ensembl.org/genome/central/">EBI</A>, - <a href="http://www.ncbi.nlm.nih.gov/Genomes/index.html">NCBI</A> - -- "Genome Hub" pages -<li><a href="http://www.ncbi.nlm.nih.gov/Sitemap/index.html">NCBI</A> -- site map to extensive services -<li><a href="http://searchlauncher.bcm.tmc.edu/">BCM</A> -- launches numerous nucleotide and protein tools -<li><a href="http://bioinfolab.unl.edu/emlab/links.html">CMS</A> -- extensive directory of tools by category -<li><a href="http://www.up.univ-mrs.fr/~wabim/english/logligne.html">ABI</A> -- very large French tool compilation -<li><a href="http://www3.oup.co.uk/nar/database/c/">NAR</A> -- curated tool collection at Nucleic Acid Research -<li><a href="http://glamdring.ucsd.edu/others/dsmith/dnasys.html#contents">UCSD</A> -- genome analysis by task area -<li><a href="http://workbench.sdsc.edu/">Workbench</A> -- unified area for searching and analysis -<li><a href="http://www.ebi.ac.uk/Tools/index.html">EMBL1</A> -- collection of database searching and tools -<li><a href="http://www.embl-heidelberg.de/Services/index.html">EMBL2</A> -- various EMBL alignment tools -<li><a href="http://picasso.ucsf.edu/mol_str_links.html">UCSF1</A>+<a href="http://www.cmpharm.ucsf.edu/cohen/links/">2</A> collections of tool links at UCSF -<li><a href="http://www.bioinf.mdc-berlin.de/">MDC</A> -- bioinformatics tools at Delbruck Center -<li><a href="http://www.ebi.ac.uk/Tools/index.html">EBI</A> -- tool and utility collection at EBI -<li><a href="http://www.sdsc.edu/Software/molbio.html">SDSC</A> -- tools at San Diego Supercomputer Center -<li><a href="http://www.bork.embl-heidelberg.de/">Bork</A> -- ten tool server of Bork lab -<li><a href="http://www.ebi.ac.uk/biocat/biocat.html">Biocatalog</A> -- bioinformatic software collection -<li><a href="http://mia.sdsc.edu">MIA</A> -- search agent finds macromolecular information -<li><a href="http://evolution.genetics.washington.edu/phylip/software.html">Phylip</A> -- tools and software for phylogenies -<li><a href="http://www.hgmp.mrc.ac.uk/Registered/Menu/phylo.html">Phylo</A> -- provides 14 utilties for phylogenetic analysis -<li><a href="http://abacus.gene.ucl.ac.uk/software/paml.html">PAML</A> -- -- maximum likelihood of evolutionary parameters and -phylogenies -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -<a name="188"><BR></a> -<!--outer table is for border purposes--> -<TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> - <TABLE BGCOLOR="fffee8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> - <TABLE BGCOLOR="D9E4F8" BACKGROUND="images/hr.gif" WIDTH=100%><TR><TD> - <!--cheap trick to get background on row to be continuous--> - <TABLE CELLPADDING=0 CELLSPACING=0 MARGIN=0 WIDTH=100%><TR><TD ALIGN="left"> - <FONT SIZE="4" ><b> Journals, Alerts, and General Internet</FONT></b></TD> - <TD ALIGN="right"><A HREF="#000"><IMG SRC="images/index.gif" ALT="Index->" BORDER=0></A> - </TD></TR></TABLE> - </TD></TR></TABLE> - <TABLE BGCOLOR="fffee8" WIDTH="100%" CELLPADDING=0><TH HEIGHT=10></TH><TR><TD><UL> -<li><a href="http://www.ncbi.nlm.nih.gov:80/entrez/jrbrowser.cgi">PubMedJB</A> -- journal browser allows access to current issues -<li><a href="http://pubcrawler.gen.tcd.ie/">PubCrawler</A> -- provides alerts to new abstracts at PubMed -<li><a href="http://highwire.stanford.edu/">HighWire</A> -- publishes online journals and provides alerts -<br><br> -<li><a href="http://www.hum-molgen.de/journals/">New Issues</A> -- provides entry to 35 genomics jounals -<li><a href="http://genomebiology.com/home/">GenomeBio</A> -- free access to post-genomics journal, pre-print server -<li><a href="http://www.pnas.org/">PNAS</A> -- free access to month-old articles in PNAS -<li><a href="http://www.jbc.org">JBC</A> -- nearly free access to most cited journal -<li><a href="http://www.sciencemag.org/">Science</A> -- high circulation general science journal -<li><a href="http://www.nature.com/">Nature</A> -- gateway to restricted spin-off journals -<li><a href="http://www.ajhg.org">AmJHumGen</A> -- leading disease gene annotation journal -<li><a href="http://www.academicpress.com/genomics">Genomics</A> -- genomics articles sometimes stale -<li><a href="http://www.genome.org/">GenomeRes</A> -- genomic research and methods articles -<li><a href="http://www.public.iastate.edu/~pedro/rt_journals.html">Pedro</A> -- large journal (and tool) collection -<br><br> -<li><a href="http://cancerweb.ncl.ac.uk/omd/">OMD</A> -- online medical dictionary -<li><a href="http://www.google.com/">Google </A> -- best internet search site for web tools -<li><a href="http://www.lycos.com/">Lycos</A> -- widely used general search tool -<li><a href="http://dir.yahoo.com/Health/News_and_Media/">Yahoo</A> -- internet categories and news -<li><a href="http://www.altavista.com/r?F09">LangTrans</A> -- useful for rough translations between languages -</UL></TD></TR></TABLE> - </TD></TR></TABLE> -</TD></TR></TABLE> - -</TD></TR></TABLE> -</BODY></HTML>