{"id":244,"date":"2023-07-10T12:25:48","date_gmt":"2023-07-10T19:25:48","guid":{"rendered":"https:\/\/live-usc-dornsife.pantheonsite.io\/pombenet\/?page_id=244"},"modified":"2023-08-06T20:51:37","modified_gmt":"2023-08-07T03:51:37","slug":"online-tools","status":"publish","type":"page","link":"https:\/\/dornsife.usc.edu\/pombenet\/online-tools\/","title":{"rendered":"PombeWeb: online tools and resources"},"content":{"rendered":"\n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <p>Useful resources around the web. These go out of date frequently, so please be sure to <a href=\"\/pombenet\/website-errors\/\">let us know if you find errors<\/a>! Check out our <a href=\"\/pombenet\/pombeweb\/\">pombeweb<\/a> page for other online pombe-ology<\/p>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n\n\n\n\n\n\n                          \n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--accordions \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--accordions\"\n    \n      >\n\n    \n  \n      <ul>\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-1-HgYHa_ZSkJ\" aria-controls=\"section-1-1-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Pombe Specific Sites and Tools<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-1-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-1-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www.pombase.org\/\">Start with Pombase,\u00a0<\/a>your source for the pombe genome.<\/li>\n<li><a href=\"http:\/\/www.bahlerlab.info\/resources\/\">J\u00fcrg Bahler&#8217;s resource page<\/a>\u00a0for transcript profiles, PCR primer programs, and more<\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/Projects\/S_pombe\/genome_stats.shtml\">Genome statistics<\/a><\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/Projects\/S_pombe\/\">The Sanger Institute<\/a>\u00a0pombe genome sequencing project.<\/li>\n<li><a href=\"http:\/\/www.genedb.org\/amigo\/perl\/go.cgi?species_db=GeneDB_Spombe\">Using the GO terminology<\/a>\u00a0to access the pombe genome sequencing project through\u00a0<strong>Amigo<\/strong><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/mapview\/map_search.cgi?taxid=4896\">Map viewer<\/a>\u00a0from NCBI. This is a great site that provides graphic clone maps and genetic and chromosome maps.<\/li>\n<li><a href=\"http:\/\/www.genedb.org\/genedb\/Pfam?organism=pombe&amp;keywords=Browse\">Pfam<\/a>\u00a0identifies protein family motifs<\/li>\n<li><a href=\"http:\/\/www.genedb.org\/amigo\/perl\/go.cgi?species_db=GeneDB_Spombe\">Predicted function\u00a0<\/a>using\u00a0<strong>Amigo<\/strong>. Also for functional classification searches. Categories agree with the\u00a0<a href=\"http:\/\/www.geneontology.org\/\">Gene Ontology Consortium<\/a>.<\/li>\n<li><a href=\"http:\/\/www.genedb.org\/genedb\/pombe\/index.jsp\">Gene name or keyword search<\/a>\u00a0through GeneDB. This is the best way to find your gene or class of interest. Use this\u00a0<a href=\"http:\/\/www.genedb.org\/gusapp\/servlet?page=boolq&amp;organism=pombe\">Boolean query tool<\/a>\u00a0for more advanced searches of GeneDB.<\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/cgi-bin\/yeastpub\/view_cosmid.p\">View cosmids with Artemis tool<\/a><\/li>\n<li><a href=\"http:\/\/www.genedb.org\/genedb2\/motifSearch?org=pombe\">Protein motif search<\/a><\/li>\n<li><a href=\"http:\/\/www.genedb.org\/genedb\/emowseSearch.jsp?organism=pombe\">eMowse<\/a>\u00a0will search the chosen protein sequence database with protein fragment information and return the protein(s) which most likely correspond to your peptide data<\/li>\n<li>Species distribution of domains: Go to the\u00a0<a href=\"http:\/\/www.sanger.ac.uk\/Pfam\">Pfam<\/a>\u00a0webpage, choose the &#8216;BROWSE PFAM&#8217; option, select a domain, and then ask to see the species distribution<\/li>\n<li>Chromosome I\u00a0status and cosmids<\/li>\n<li>Chromosome II\u00a0status and cosmids<\/li>\n<li>Chromosome III\u00a0status and cosmids<\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/PostGenomics\/S_pombe\/\">Functional genomics<\/a>\u00a0at the Sanger Institute&#8211;DNA microarrays!<\/li>\n<li>Check out the recently released\u00a0S. japonicus sequence<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-2-HgYHa_ZSkJ\" aria-controls=\"section-1-2-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Expression<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-2-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-2-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www.bahlerlab.info\/resources\/\">Gene Expression Viewer<\/a>\u00a0from Jurg Bahler, which contains the data from meiotic, cell cycle, and stress expression expts.<\/li>\n<li>Microarrays at SUNY\u00a0available to the community<\/li>\n<li>S. pombe epigenome page\u00a0from Shiv Grewal<\/li>\n<li><a href=\"ftp:\/\/ftp.sanger.ac.uk\/pub\/yeast\/pombe\/Intron_Data\/\">ftp:\/\/ftp.sanger.ac.uk\/pub\/yeast\/pombe\/Intron_Data\/<\/a><\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/Projects\/S_pombe\/DNA_download.shtml\">manual map of UTRs on genome sequence<\/a><\/li>\n<li>S. pombe is now included in the\u00a0<a href=\"http:\/\/www.ucmb.ulb.ac.be\/bioinformatics\/rsa-tools\/\">Regulatory Sequence Analysis Tools<\/a>\u00a0(RSAT) website. This site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.<\/li>\n<li><a name=\"primer\"><\/a>Primer design\u00a0<a href=\"http:\/\/www.sanger.ac.uk\/PostGenomics\/S_pombe\/software\">Web-interface scripts<\/a>\u00a0that automatically design primers for PCR-based gene targeting. (Click link for &#8220;software&#8221;). This will automatically suggest primer sequences for gene deletion, tagging, and\/or regulatable expression based on gene name and plasmid information that you specify. It will now design large primers for gene targeting and small primers upstream and downstream for monitoring integration.<\/li>\n<li>How to delete a pombe gene in 8 days\u00a0will design primers for any ORF<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-3-HgYHa_ZSkJ\" aria-controls=\"section-1-3-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Other sites<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-3-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-3-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www.nih.gov\/science\/models\/Schizosaccharomyces\/index.html\">NIH S. pombe page<\/a>: The Trans-NIH S. pombe initiative.<\/li>\n<li>FYSSION: pombe strain resources at Sussex.<\/li>\n<li>Yeast Genetic Resource Center Japan.\u00a0: pombe strain resources in Japan.<\/li>\n<li>Transposon sequences in pombe\u00a0includes coordinates of LTRs and LTR fragments<\/li>\n<li>This\u00a0online program\u00a0predicts introns and exons.<\/li>\n<li>GFP fusion library images of intracellular localisations are now available on the web at\u00a0http:\/\/www-karc.crl.go.jp\/bio\/CellMagic\/index.html<\/li>\n<li>Also see the\u00a0S. pombe post genome database\u00a0with results from a systematic analysis of protein expression and localization.<\/li>\n<li>Pedent\u00a0automated protein analysis of S. pombe at MIPS.<\/li>\n<li>The NIH Genobase pombe gene list, for known genes<\/li>\n<li>Swiss Prot pombe entries<\/li>\n<li><a href=\"http:\/\/www.bis.med.jhmi.edu\/Dan\/fields\/pir\/species\/schizosaccharomycespombe.html\">PIR search<\/a>\u00a0for pombe proteins<\/li>\n<li>download all current\u00a0pombe entries\u00a0in Genbank<\/li>\n<li>tRNA scan analysis of S. pombe genome<\/li>\n<li><a href=\"http:\/\/www.cbs.dtu.dk\/services\/GenomeAtlas\/Eukaryotes\/Schizosaccharomyces\/pombe\/972h-\/\">DNA structural analysis<\/a><\/li>\n<li>Proteome analysis at EBI<\/li>\n<li><a href=\"\/pombenet\/gene-conversion-table\/\">Gene conversion table<\/a>\u00a0lists budding yeast homologues of (some) fission yeast genes.<\/li>\n<li><a href=\"\/pombenet\/working-with-pombe\/\">Restriction site usage<\/a>\u00a0in pombe genome<\/li>\n<li>codon usage\u00a0in S. pombe<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-4-HgYHa_ZSkJ\" aria-controls=\"section-1-4-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">TAP tagging resources<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-4-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-4-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li>Gould lab TAP-tag page<\/li>\n<li>Juraj Gregan&#8217;s\u00a0<a href=\"http:\/\/mendel.imp.ac.at\/Pombe_tagging\/\">Tap Tagging any ORF in pombe<\/a>\u00a0page<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-5-HgYHa_ZSkJ\" aria-controls=\"section-1-5-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Other<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-5-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-5-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li>Pombe community news<\/li>\n<li><a href=\"\/pombenet\/pombeweb\/\" target=\"_self\">Pombeweb<\/a>\u00a0: homepages and more<\/li>\n<li>Whitepaper from the Broad Institute\u00a0on sequencing other Schizosaccharomyces sp.<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-6-HgYHa_ZSkJ\" aria-controls=\"section-1-6-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">General Organizations and Sites<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-6-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-6-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<p>Also see\u00a0<a href=\"\/pombenet\/online-tools\/\">pombe specific sites<\/a><\/p>\n<ul>\n<li><a href=\"http:\/\/www.genecards.org\/\">Genecards,<\/a>\u00a0for cross-species orthologues<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/\">NCBI<\/a><\/li>\n<li>NIH model organisms page<\/li>\n<li>Saccharomyces Genome Database<\/li>\n<li><a href=\"http:\/\/www.genedb.org\/genedb\/pombe\/index.jsp\">GeneDB<\/a>, a friendly front end to the pombe data from the Sanger<\/li>\n<li>Tutorial on Pfam\u00a0from the Sanger<\/li>\n<li><a href=\"http:\/\/genome.jgi-psf.org\/chlre1\/chlre1.home.html\">Chlamydomonas\u00a0<\/a>genome site. aka &#8220;green yeast&#8221;<\/li>\n<li>Genomics\u00a0page from Wiley publishing includes\u00a0genomics community links<\/li>\n<li><a href=\"http:\/\/www.tigr.org\/tigr_home\/index.html\">TIGR<\/a><\/li>\n<li><a href=\"http:\/\/www.sciencemag.org\/feature\/plus\/sfg\/\">Science Functional Genomics<\/a>\u00a0from Science Magazine<\/li>\n<li>Proteome, for YPD and pombePD<\/li>\n<li><a href=\"http:\/\/www.genecards.org\/\">Genecards<\/a>\u00a0for human genes, includes lists of orthologues<\/li>\n<li><a href=\"http:\/\/www.nature.com\/ng\/web_specials\/gazing\/\">Review of sequence gazing<\/a>\u00a0from Nature Genetics<\/li>\n<li>GOLD: Genomes OnLine Database<\/li>\n<li>vector DB\u00a0at Stanford, has vector sequences.<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-7-HgYHa_ZSkJ\" aria-controls=\"section-1-7-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Sequence Comparisons<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-7-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-7-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/BLAST\/Genome\/YeastBlast.html\">BLAST<\/a>\u00a0both yeast genomes at once (NCBI)<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/BLAST\/\">NCBI BLAST<\/a><\/li>\n<li>Blitz search<\/li>\n<li><a href=\"http:\/\/blast.wustl.edu\/\">WUSTL Blast archive<\/a><\/li>\n<li>Organism specific search engines<\/li>\n<li>SRS-FASTA<\/li>\n<li><a href=\"http:\/\/www.sanger.ac.uk\/Projects\/S_pombe\/blast_server.shtml\">pombe Blast server<\/a>\u00a0(UK)<\/li>\n<li><a href=\"http:\/\/133.63.36.123\/sindex.html\">S. pombe cDNA blast server<\/a>\u00a0(Japan)<\/li>\n<li>Saccharomyces Blast server<\/li>\n<li>C. elegans blast server 1\u00a0and\u00a02, from the Sanger Institute, or from\u00a0WUSTL<\/li>\n<li>Yeast blast\u00a0from NCBI<\/li>\n<li>consensus sequence zen<\/li>\n<li><a href=\"http:\/\/dcc.icgc.org\/\">ICGC data portal<\/a>\u00a0for genes mutated in cancer<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-8-HgYHa_ZSkJ\" aria-controls=\"section-1-8-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Sequence Analysis Tools and Searches<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-8-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-8-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Genbank\/GenbankSearch.html\">Searching genbank<\/a><\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Tools\/index.html\">database mining tools from NCBI<\/a><\/li>\n<li>Research tools\u00a0from SDSC<\/li>\n<li><a href=\"http:\/\/meme.sdsc.edu\/meme\/website\/\">MAST<\/a>, useful for distant homologues<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Structure\/lexington\/lexington.cgi?cmd=rps\">DART<\/a>: The Domain Architecture Retrieval Tool allows for protein neighboring by domain architecture. Use pre-calculated CD-Search results to find proteins which contain a set of domains similar to that of your query.<\/li>\n<li>Expasy<\/li>\n<li>Pedro&#8217;s Research Tools<\/li>\n<li><a href=\"http:\/\/www.expasy.ch\/tools\/\">Expasy proteomics tools<\/a><\/li>\n<li>Bioinformatics accelerator list\u00a0(at Stanford)<\/li>\n<li>MBCR database links<\/li>\n<li>BCM search launcher<\/li>\n<li><a href=\"http:\/\/www.embl-heidelberg.de\/predictprotein\/predictprotein.html\">protein structure prediction<\/a><\/li>\n<li>WUSTL sequence center<\/li>\n<li><a href=\"http:\/\/www.embl-heidelberg.de\/srs5\/\">seq retrievel service<\/a><\/li>\n<li>comp biol at NIH (links and tools)<\/li>\n<li><a href=\"http:\/\/www.geneontology.org\/\">Gene Ontology Consortium<\/a>\u00a0for functional categories<\/li>\n<li>Expasy proteomics tools list<\/li>\n<li>How to read a sequence logo<\/li>\n<li>how to make\u00a0a sequence logo (download and compile)<\/li>\n<li><a href=\"http:\/\/weblogo.berkeley.edu\/\">how to make<\/a>\u00a0a sequence logo (webserver)<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-9-HgYHa_ZSkJ\" aria-controls=\"section-1-9-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Protein Domains<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-9-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-9-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/smart.embl-heidelberg.de\/\">SMART<\/a>\u00a0database at EMBL. Start here for domains!<\/li>\n<li><a href=\"http:\/\/string.embl.de\/\">String database<\/a>\u00a0at EMBL, summarizes interactions.<\/li>\n<li>Conserved domain database, Pawson Lab Domains Database<\/li>\n<li><a href=\"http:\/\/pfam.wustl.edu\/index.html\">Pfam<\/a>\u00a0from WUSTL. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families. From here you can link into\u00a0<a href=\"http:\/\/www.rio.wustl.edu\/\">Rio<\/a>. Given a query sequence, Pfam domain, and species, the RIO server will order sequences in the Pfam domain by orthology to the query. Many other options are available, and an annotated gene tree can be generated and viewed with ATV. Check out\u00a0<a href=\"http:\/\/www.sanger.ac.uk\/Users\/rdf\/PombeTutorial\/\">this tutorial<\/a>\u00a0on PFAM from the Sanger.<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Structure\/cdd\/cdd.shtml\">Conserved domain database<\/a><\/li>\n<li>Blocks\u00a0including Blocksearcher and Blockmaker<\/li>\n<li><a href=\"http:\/\/scansite.mit.edu\/\">Scan site<\/a>\u00a0from MIT.<\/li>\n<li>Prosite<\/li>\n<li><a href=\"http:\/\/scop.berkeley.edu\/\">SCOP<\/a>\u00a0allows structural classification<\/li>\n<li>Nuclear localization sequence server; also see this list of\u00a0known NLSes<\/li>\n<li>Pestfind, to locate PEST sequences<\/li>\n<li>Multiple alignment server<\/li>\n<li>boxshade server<\/li>\n<li>Multi align<\/li>\n<li>Regulatory Sequence Analysis Tools\u00a0(RSAT) website provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.<\/li>\n<li><a href=\"http:\/\/evolution.genetics.washington.edu\/phylip.html\">Phylip<\/a>\u00a0allows you to build trees (dendrograms) from alignment data<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-10-HgYHa_ZSkJ\" aria-controls=\"section-1-10-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Homologues<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-10-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-10-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li><a href=\"http:\/\/www2.ebi.ac.uk\/ppsearch\/\">PP search<\/a><\/li>\n<li>XREF-DB\u00a0(model organisms vs. human disease genes)<\/li>\n<li><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/Genbank\/GenbankSearch.html\">NCBI search page<\/a><\/li>\n<li><a href=\"http:\/\/www.genome.ad.jp\/dbget\/dbget.links.html\">Database map<\/a>\u00a0(BRITE)<\/li>\n<li><a href=\"https:\/\/dornsife.usc.edu\/pombenet\/gene-conversion-table\/\">Gene coversion table<\/a>\u00a0for pombe and cerevisiae genes.<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-11-HgYHa_ZSkJ\" aria-controls=\"section-1-11-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Large Data Sets<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-11-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-11-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li>genequiz\u00a0from the EBI gives access to functional data across genomes&#8211;helps you find out what your protein does based on comparisons to many complete genomes.<\/li>\n<li><a href=\"http:\/\/biodata.mshri.on.ca\/grid\/servlet\/Index\">GRID<\/a>: General Repository for Interaction Datasets (for S. cerevisaie). The GRID is a database of genetic and physical interactions developed in The Tyers Group at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital. It contains interaction data from many sources, including several genome\/proteome-wide studies, the MIPS database, and BIND. includes Osprey, a software tool to visualize interactions.<br \/>\nA project to record published fission yeast genetic and physical interactions is underway with Mike Tyers and the\u00a0<a href=\"http:\/\/biodata.mshri.on.ca\/grid\/servlet\/Index\">GRID<\/a>\u00a0group at Toronto. A sample page is\u00a0<a href=\"http:\/\/biodata.mshri.on.ca\/pombe_grid\/servlet\/SearchPage\">here<\/a>. If you are interested in participating either in direct data entry of your favorite genes, or in assisting in quality control after the data entry is complete, please email Val Wood\u00a0<i>val (AT) SANGER (DOT) A C (DOT) U K<\/i>\u00a0to join the pombe GRID mailing list.<\/li>\n<li>Meta analysis of coexpression data\u00a0from the Kim lab. This group compared data from microarray experiments across four eukaryotic species and looked for gene pairs that were coexpressed. This site has the supplemental data from their\u00a0<a href=\"http:\/\/www.sciencemag.org\/cgi\/content\/abstract\/1087447v1?ijkey=\/KO4rBc1KfHIY&amp;keytype=ref&amp;siteid=sci\">Science paper<\/a> which you can search for your favorite genes.<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-12-HgYHa_ZSkJ\" aria-controls=\"section-1-12-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Budding Yeast Resources<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-12-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-12-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li>Yale Genome resources<\/li>\n<li>Yeast resource Center\u00a0for protein analysis (microscopy, 2 hybrid, mass spec)<\/li>\n<li>Saccharomyces Genome Database<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-13-HgYHa_ZSkJ\" aria-controls=\"section-1-13-HgYHa_ZSkJ\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">Software<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-13-HgYHa_ZSkJ\" role=\"region\" aria-labelledby=\"heading-1-13-HgYHa_ZSkJ\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n      \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <div class=\"html-content\">\n<ul>\n<li>Sequence Analysis Software<\/li>\n<li><a href=\"http:\/\/biodata.mshri.on.ca\/osprey\/servlet\/Index\">OSprey<\/a>\u00a0is a viewer for protein interaction data<\/li>\n<li>Biological Software Resources<\/li>\n<\/ul>\n<\/div>\n\n\n\n<\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n          <\/ul>\n  \n  \n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":354,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-244","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - 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