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    Archived pages: 157 . Archive date: 2014-06.

  • Title: Saccharomyces Genome Database
    Descriptive info: .. Saccharomyces Genome Database.. About.. Blog.. Download.. Site Map.. Help.. Email Us.. Twitter.. Facebook.. YouTube.. RSS.. YeastMine:.. Batch Analysis.. or.. Advanced Search.. SGD.. Menu.. Analyze.. Gene Lists.. BLAST.. Fungal BLAST.. GO Term Finder.. GO Slim Mapper.. Pattern Matching.. Design Primers.. Restriction Mapper.. Sequence.. Genome Browser.. Gene/Sequence Resources.. Reference Genome.. Download Genome.. Genome Snapshot.. Chromosome History.. Systematic Sequencing Table.. Original Sequence Papers.. Strains and Species.. Align Strain Sequences.. Synteny Viewer.. Homology.. Fungal Alignment.. PDB Search.. Resources.. UnikProtKB (EBI).. InterPro (EBI).. HomoloGene (NCBI).. YGOB (Trinity College).. Function.. GO.. GO Slim Mapping File.. Expression.. Biochemical Pathways.. Phenotypes.. Browse All Phenotypes.. Interactions.. YeastGFP.. GO Consortium.. BioGRID (U.. Toronto).. Literature.. Full-text Search.. New Yeast Papers.. YeastBook.. Genome-wide Analysis Papers.. PubMed (NCBI).. PubMed Central (NCBI).. Google Scholar.. Community.. Colleague Information.. Find a Colleague.. Add or Update Info.. Find a Yeast Lab.. Career Resources.. Meetings.. Future.. Yeast Genetics.. Nomenclature.. Submit a Gene Registration.. Gene Registry.. Nomenclature Conventions.. Global Gene Hunter.. Methods and Reagents.. Strains and Constructs.. Reagents.. Protocols and Methods.. Historical Data.. Physical Genetic Maps.. Genetic Maps.. Gene Summary Paragraphs.. Wiki.. Info Downloads.. Downloads.. Floccule of yeast rho0 cells expressing PTS1-GFP as a peroxisomal marker, stained with calcofluor white.. Image courtesy of Dr.. Jakob Vowinckel, University of Cambridge.. Localization of active Ras in a wild type strain.. Image courtesy of S.. Colombo and E.. Martegani, University Milano Bicocca.. Sectored colonies showing loss of silencing at the HML locus.. Image courtesy of Anne Dodson, UC Berkeley.. Pma1p imaged using the RITE tagging system in mother (green) and daughter cells (red).. Image courtesy of Dan Gottschling Ph.. D.. , Fred Hutchinson Cancer Research Center.. Lipid droplets in.. fld1.. mutant images by CARS.. Image courtesy of Heimo Wolinski, Ph.. and Sepp D.. Kohlwein, Ph.. , University of Graz, Austria.. Fpr3p accumulation in the nucleolus of.. S.. cerevisiae.. Image courtesy of Amy MacQueen, Ph.. , Wesleyan University.. anti-Fpr3 antibody courtesy of Jeremy Thorner, Ph.. , UC Berkeley.. San1 strain visualized with FUN and calcofluor white.. Image courtesy of the Bruschi lab, ICGEB, Trieste, Italy.. Single.. MDN1.. mRNAs detected by FISH.. Image courtesy  ...   06/19/2014.. In the Matrix Trilogy, the delicate balance of a virtual world is upset by a rogue computer program that goes by the name of Agent Smith.. This program finds and touches other agent programs, converting them into copies of itself.. Eventually, all the agent programs are copies of Agent Smith and only the hero Neo can save humanity in an epic battle within the virtual world of the Matrix.. A new study out in GENETICS by.. Read.. Holding Back the Translation Torrent.. 06/12/2014.. We all know the story of the little Dutch boy who stuck his finger into a hole in a dike to keep his village from being flooded.. Now, a new study out in Molecular Cell by Pircher and coworkers has identified a novel regulatory mechanism involving a small 18-nucleotide RNA that behaves similarly to this boy.. A big difference in our story is that unlike the broken dike, the “water flow” in yeast cells is usually a good thing.. It.. Saddling Mom with the Burden of Old Age.. 06/05/2014.. In A World Out of Time by Larry Niven, people live forever by teleporting the unfolded protein aggregates associated with aging out of their cells.. Turns out that our very clever yeast Saccharomyces cerevisiae can do the same thing and it doesn’t need a machine.. Instead of teleporting the aggregates away, yeast saddles the mother cell with them when it buds.. The daughter has now regained her youth and the mother is left to struggle with old age.. In.. Professor Jure Piskur, Ph.. (1960 - 2014).. 06/04/2014.. Dr.. Jure Piskur, Professor and Carlsberg Foundation Chair in Molecular Food Microbiology at Lund University, sadly passed away on May 18, 2014.. Piskur worked on yeast early in his scientific career, including postdoctoral research in yeast molecular biology at Carlsberg Brewery.. From there, he studied Drosophila genes involved in the metabolism of nucleic acid precursors as well as yeast biodiversity and mitochondrial genetics.. Most recently, his research focused on genes involved.. Previous articles >>>.. Terms of Use.. Stanford University, Stanford, CA 94305..

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  • Title: About : Saccharomyces Genome Database
    Descriptive info: About Yeast.. What are yeast, anyway? Get a general introduction to yeast and its uses on our ".. What are yeast?.. " page, found in the.. SGD Community Wiki.. Genome Database (SGD,.. http://www.. yeastgenome.. org.. ) is the community resource for the budding yeast.. The SGD project provides encyclopedic information about the yeast genome and its genes, proteins, and other encoded features.. Experimental results on the functions and interactions of yeast genes, as reported in the peer-reviewed literature, are extracted by high-quality manual curation and integrated within a well-developed database.. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine, and a rich genome browser.. This complex collection of information is integrated with a variety of bioinformatic tools to facilitate experimental design and analysis and allow productive discovery of new biological details.. The SGD resource provides the gold standard for functional description of budding yeast, and a platform from which to investigate related genes and pathways in higher organisms.. SGD also serves the yeast research community by maintaining the reference genomic chromosomal sequence, overseeing.. genetic nomenclature, functioning as a central hub for researchers to  ...   by the NHGRI [2U41HG002273-13] and the InterMOD project [5R01HG004834-04].. The SGD is part of the.. Department of Genetics.. at the School of Medicine, Stanford University and located within the Center for Genomics and Personalized Medicine.. Viewing SGD.. SGD is best viewed with a recent version of Chrome, Safari or Firefox with javascript enabled.. Contacting SGD.. Please send comments or questions to the SGD project via this.. form.. Alternatively, email us at sgd-helpdesk@lists.. stanford.. edu or call us at (650) 725-8956.. Biocuration.. How to Cite SGD.. SGD Publications.. SGD Newsletter Archives.. Scientific Advisory Board.. SGD Staff Members.. Technical Specifications.. Curated Data.. Genomics.. Published Datasets.. Unpublished Data.. Database.. Reference Library.. Video Tutorials.. Basic Navigation.. YeastMine.. General Features.. Getting Started.. Search SGD.. Glossary.. Locus Summary Page.. Locus History.. YeastGenome App Information.. Reference Sequence.. PDB Homologs.. All Associated Sequences.. Chromosomal Features Map.. Gene Ontology (GO).. Regulation.. Protein Information.. Literature Guide.. Curated Paper.. Find a yeast lab.. Physical and Genetic Maps.. Yeast Mortimer Maps Edition 12.. Chromosome I.. Chromosome II.. Chromosome III.. Chromosome IV.. Chromosome V.. Chromosome VI.. Chromosome VII.. Chromosome VIII.. Chromosome IX.. Chromosome X.. Chromosome XI.. Chromosome XII.. Chromosome XIII.. Chromosome XIV.. Chromosome XV.. Chromosome XVI..

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  • Title: Blog : Saccharomyces Genome Database
    Descriptive info: June 19, 2014.. In the.. Matrix Trilogy.. , the delicate balance of a virtual world is upset by a rogue computer program that goes by the name of Agent Smith.. Prions are the Agent Smiths of cells.. They convert healthy proteins into prions just by touching them.. Image by Marcin Wichary.. A new study out in.. GENETICS.. by.. Li and Du.. provides additional evidence that prions in the yeast.. work similarly to Agent Smith, in that they spread through a direct contact model.. These prions are proteins that have entered a rogue conformation, and they end up converting all copies of the same protein into a similar rogue conformation.. The proteins change from a hardworking Agent Smith trying to do its job into something that mucks up the working of a cell.. And the results, at least in humans, can be as catastrophic for the cell as Agent Smith was for the Matrix.. Mad cow disease, for example, is caused by prions converting the prion protein (PrP) in the brain cells of people from a useful conformation to a dangerous one that spreads.. As the conformation spreads throughout the cell, these prions form amyloid fibrils that eventually kill the cell.. When enough brain cells are killed, the person dies.. The authors chose to work in yeast because unlike in people, there are multiple examples of proteins in yeast that can go prion.. The list includes.. Sup35p.. ,.. Ure2p.. Rnq1p.. Swi1p.. Cyc8p.. Mot3p.. Sfp1p.. Mod5p.. and.. Nup100p.. As you might guess from the sheer number of these prion-ready proteins, prions actually do more than kill a cell in yeast; they can serve useful functions.. Scientists have yet to identify any useful functions for the prion form of PrP in people.. Having multiple prions in a cell allowed Li and Du to perform some experiments to try to distinguish between two models of prion conformation spreading.. In the first, called the cross-seeding model, the prion acts very much like Agent Smith in that it needs to contact a “healthy” protein to convert it into a prion.. In the second model, the titration model, factors in the cell that prevent prion formation are titrated out when prions form.. As the factors are taken out of commission, prions are free to form.. The main evidence in this study that supports the cross-seeding model has to do with the localization of pre-existing prions during the de novo formation of a new prion.. Li and Du found that the prion [SWI+] localized to newly forming [PSI+] prions but not to already formed [PSI+] prions.. This is not the result we would expect if prion formation were due to titrating out of inhibitors of prion formation.. If that were the mechanism, then there would be no reason for [SWI+] to colocalize with newly forming [PSI+].. These experiments are like having a google map of the Matrix where we could see Smiths converting other agents by touch and then moving on and touching other agents.. Work like this is important for helping to find treatments for prion associated diseases and, perhaps, other amyloid fibril forming diseases like Huntington’s or Alzheimer’s.. Scientists need to focus on the amyloid fiber forming proteins themselves instead of trying, for example, to ramp up the activity of factors that inhibit formation.. Scientists probably need to eliminate Agent Smith to prevent the destruction of the Matrix and all of mankind.. This is how prions turn other proteins into copies of themselves:.. Category:.. Research Spotlight.. Tags:.. prions.. >.. Holding Back the Translation Torrent.. June 12, 2014.. Now, a new study out in.. Molecular Cell.. Pircher and coworkers.. has identified a novel regulatory mechanism involving a small 18-nucleotide RNA that behaves similarly to this boy.. The little Dutch boy used his finger, but yeast can stop the mighty torrent of translation using only a tiny noncoding RNA.. Image from Wikimedia Commons.. It is the continuous stream of protein translation that goes through the ribosome.. When it’s under stress, though, yeast needs to slow down translation in order to make sure that it is making and folding each protein correctly.. This gives it a better shot at surviving the stress.. Once the stress is gone, translation can ramp up again.. This is where that 18-nt RNA comes in.. This group identified this 18-nt RNA as a ribosome binding RNA in a previous study.. Because there are only a couple of known cases where a noncoding RNA  ...   of Old Age.. June 5, 2014.. In.. A World Out of Time.. by Larry Niven, people live forever by teleporting the unfolded protein aggregates associated with aging out of their cells.. Turns out that our very clever yeast.. Saccharomyces cerevisiae.. can do the same thing and it doesn’t need a machine.. Yeast cells don’t need a teleporter to eliminate age-related protein bundles.. They just leave them with mom and use a caspase to chew up the rest.. Image by Chris Radcliff.. In a new study in.. Science.. Hill and coworkers.. show that the yeast metacaspase gene.. MCA1.. is critical in this process.. But it doesn’t look like it is involved in segregating these bundles to the mother cell.. Instead, it appears to help clear away many of the bundles left in the daughter.. If it were in Niven s original story, Mca1p might be a little nanobot that chewed up any aggregates the teleporter missed.. This all makes sense given caspases’ role in multicellular beasts.. There, these executioner proteases chew up cellular proteins during.. apoptosis.. , the process of programmed cell death that is a critically important part of development and growth.. Although apoptosis has been observed in yeast and Mca1p is involved in the process, it has always been a bit of a mystery why a single-celled organism needs a mechanism for suicide.. This study now suggests that yeast’s only caspase, Mca1p, has a role as a healer as well as an executioner.. It saves the daughter by degrading and proteolytically clearing away the aggregated bundles clogging up her cell.. Scientists already knew that.. HSP104.. was a key player in making sure that aggregates stayed with mom.. Hill and coworkers used this fact and performed a genetic interaction screen using.. to identify.. as required to keep protein aggregates out of the daughter in response to a heat shock.. Follow up work confirmed this result by showing that overexpressing.. led to more efficient segregation of aggregates and that deleting it led to poor segregation of aggregates.. Digging deeper, these authors found that this poor segregation was because Mca1p was not eliminating aggregates in the daughter, as opposed to affecting the segregation itself.. They also showed that the protease activity of Mca1p was needed for this effect.. In the final set of experiments we’ll discuss, the authors looked to see what effect.. has on the life span of a yeast cell.. They saw little effect of deleting.. unless a second gene was also deleted:.. YDJ1.. , which encodes an HSP40 co-chaperone.. The double deletion mutant yeast were able to divide fewer times before petering out.. Consistent with this, overexpressing.. led to increased life span and this effect was enhanced in the absence of.. Finally, cells lived for a shorter time if just the active site of the Mca1p protease was compromised in a.. ydj1.. deletion background.. This again confirms that proteolysis is key to.. ’s effects on aging.. So yeast attains eternal youth by both dumping its age-related aggregates on its mother and by using Mca1p to destroy any aggregates that managed to get into the daughter.. The daughter gets a reset until she builds up too many aggregates, in which case she gets saddled with them.. Yeast may be showing us another way to live a longer life.. If we can specifically degrade our aggregates without causing our cells to commit mass suicide, maybe we can extend our lives.. And we don’t even need fancy teleporting machinery; we just need to adapt the molecular machinery yeast is born with.. Feel free to use this idea for a new science fiction story!.. ageing.. caspase.. protein aggregates.. (1960 2014).. June 4, 2014.. Jure Piskur, 1960-2014.. From there, he studied.. Drosophila.. genes involved in the metabolism of nucleic acid precursors as well as yeast biodiversity and mitochondrial genetics.. Most recently, his research focused on genes involved in the metabolism of nucleic acid precursors and the evolution and molecular mechanisms which reshaped the modern enzymes and yeast genomes.. Piskur published many scientific papers, many of them.. represented.. in SGD.. He was also a.. FEMS.. Microbiology Reviews Editor and Yeast Research Editorial Board Member.. For more information on Dr.. Piskur, please view his Lund University.. profile page.. News and Views.. Next Page.. Recent Posts.. Create, Analyze, Save: the Power of Gene Lists in YeastMine.. Categories.. Conferences.. Data updates.. New Data.. Newsletter.. Tutorial.. Uncategorized.. Website changes.. Yeast and Human Disease.. Archives.. 2014.. 2013.. 2012.. 2011..

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  • Title: Download Data : Saccharomyces Genome Database
    Descriptive info: Data at SGD can be downloaded in multiple ways:.. From.. , a powerful search and retrieval tool that allows for sophisticated queries and download in customizable user-defined formats.. From individual pages.. For example, via the 'Download Data' link on the phenotypes or interactions pages.. In pre-defined formats available from our Downloads server:.. - genes, proteins, identifiers, functional annotations,  ...   stricto.. species.. - comparative analysis results.. - data files from SGD's expression analysis tool SPELL (Serial Pattern of Expression Levels Locator).. - datasets and supplemental data files curated at SGD, including high-throughput data.. - historical data from retired yeast tools and unpublished analyses.. - SQL schema definition files that specify the SGD Oracle database.. - miscellaneous historical reference data..

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  • Title: Site Map : Saccharomyces Genome Database
    Descriptive info: The SGD site map provides links to the major resources and tools in SGD.. Home.. Gene / Sequence Resources.. Original sequence papers.. Strains and species.. UniProtKB (EBI).. Search for phenotypes.. Browse all phenotypes.. Yeast Genetics Meetings.. WIki..

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  • Title: Help : Saccharomyces Genome Database
    Descriptive info: SGD maintains help documentation for tools and data types.. Help pages for individual tools can be accessed via the question mark symbol found in the upper right section of that page.. Help pages are context dependent; the link will point to documentation for the page you are viewing.. Tutorials.. - short tutorials describing specific aspects of various SGD tools and features, including Biochemical Pathways, the YeastMine data search tool, the  ...   - getting started in SGD, finding information about your favorite genes, what's known about the.. genome, glossary of terms.. - DNA or protein sequences, function annotation, primers, restriction maps.. - find and retrieve, compare strains and species, chromosome history, reference genome.. - interactions, phenotypes, localization, expression, regulation, pathways.. - search full text, find new papers, genome-wide analysis papers.. - colleagues, job postings, meetings, reserve gene names, genetic maps, and more..

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  • Title: Yeast Phenotype Ontology | SGD
    Descriptive info: Yeast Phenotype Ontology.. Summary.. Description:.. Features of.. cells, cultures, or colonies that can be detected, observed, measured, or monitored.. Ontology Diagram..

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  • Title: Blog : Saccharomyces Genome Database
    Descriptive info: May 30, 2014.. If you love to make and analyze lists of genes, you will love.. – you can use it to create all kinds of lists! For instance, use a YeastMine.. template.. to search for all genes associated with a given GO term or phenotype observable and save these genes as a list.. Or, search for all genes that interact with your gene of interest and save that as a gene list.. What’s even more fun is that you can make lists from your lists! For instance, take the list of genes you found to be associated with a given GO term and plug it into a YeastMine query template to find all the genes that interact with your list of genes – then save those genes as a list.. The possibilities are endless given the different types of queries you can perform using YeastMine! Who knows what biological connections you will uncover?.. Lastly, save your lists for future use by creating a.. MyMine account.. – all you need to sign up is an email and a password.. You can find a link to YeastMine in the top right corner of most SGD pages ( YeastMine: Batch Analysis or Advanced Search ) or go to SGD s purple main menu bar, click on Analyze and select Gene Lists to go straight to creating a List in YeastMine.. To see how simple it is to save your search results as a List in YeastMine, view this brief tutorial.. YeastMine: Saving Search Results as a List.. To view other great SGD tutorials, YeastMine and otherwise, visit and Subscribe to the.. Saccharomyces Genome Database Channel.. on YouTube.. Slipping Through Haldane’s Sieve.. May 22, 2014.. Just as harsh panning can uncover hidden gold nuggets, so too can loss of heterozygosity reveal beneficial new recessive mutations.. Image via Wikimedia Commons.. Imagine you are panning for gold in a river and there are two kinds of nuggets.. One type is naked gold while the other is gold hidden inside of normal rock.. Pretty easy to figure out which nuggets you’ll gather first!.. Now imagine instead that the process of panning is a rough one that knocks the shell off of the second type of nugget revealing the gold inside.. Now there won’t be any difference between the two.. You will be just as likely to keep both types of nuggets.. The same sort of situation applies to new beneficial mutations in a changing environment.. Back in 1927,.. J.. B.. Haldane.. predicted that the more dominant a mutation, the more likely it was to help a diploid beast adapt to a new environment.. The naked gold was more likely to be taken over the covered gold.. Gerstein and coworkers.. show in a new study that at least in the yeast.. , Haldane’s sieve (as it is called) may not always apply.. The process of adapting to a new environment can strip away the dominant older allele, revealing the recessive one.. Loss of heterozygosity (LOH) uncovers the hidden gold of the recessive phenotype.. The authors had previously identified haploid mutants that were able to survive in the presence of the fungicide nystatin.. They mated these mutants to create either heterozygotes or homozygous recessive mutants and compared these to wild-type diploids growing either in the presence or absence of nystatin.. Gerstein and coworkers found a wide range of effects of these mutations in the absence of nystatin.. Sometimes heterozygotes grew better than either homozygote, sometimes homozygous recessive strains did best, and sometimes wild type grew best.. Phenotypes were all over the map.. The story was very different in the presence of nystatin where only the homozygous recessives managed to grow.. This appears to contradict Haldane’s sieve.. Here there were no dominant mutations that allowed for survival.. Gerstein and coworkers found  ...   short time.. We will make every effort to minimize any downtime associated with this maintenance.. We apologize for any inconvenience this may cause, and we thank you for your patience and understanding.. Yeast: A One Man Band for Finding New Drug Leads.. May 15, 2014.. Yeast has been turned into a one man band that makes and assays its own drug leads.. Imagine you are in a band and the only instruments you have are guitars.. Yes, you can play.. some beautiful music.. , but there will be a whole lot of music that your band won’t be able to play.. In some ways, finding chemical leads to develop into drugs is similar to an all guitar band.. The compounds in available libraries all tend to have a lot in common.. They are like a vast array of subtly different guitars.. In a new study,.. Klein and coworkers.. use synthetic biology to have the yeast.. make more varied libraries on its own.. As an added bonus, the authors also use the yeast to assay the new leads.. Not only have they expanded the range of instruments available to your band, but they’ve also made it so you can play all the instruments.. You are now a one man band!.. The first step in all of this is to have an assay that can easily pick out the important leads.. Klein and coworkers use a galactose inducible Brome Mosaic Virus (BMV) system they had previously developed.. In this system, if one of the viral genes is on, then it produces a fusion protein that includes the.. Ura3.. protein.. When the.. URA3.. gene is expressed, yeast die in the presence of 5-fluoroorotic acid (5-FOA).. So any yeast that can make a compound that can inhibit viral expression will survive in 5-FOA.. The next step in creating these.. in vivo.. libraries was to randomly assemble various biochemical pathways into yeast artificial chromosomes (YACs) and to transform them into yeast.. These pathways were chosen because they have yielded important compounds before or because they come from medically important beasts.. This work was described in detail in a.. previous paper.. Specifically, Klein and coworkers randomly combined cDNA genes from eight biochemical pathways into YACs and transformed them into the BMV replication yeast strain.. They found 74 compounds that allowed the yeast to survive in the presence of 5-FOA.. Of these, 28 had activity in a secondary BMV assay.. A close look at the 74 compounds showed that by and large, most had characteristics that put them in the right ballpark to be useful leads.. They had low molecular weight and the right hydrophobicity, and were chemically complex.. In addition, many could easily be improved chemically (this last point is called optimizability).. Most importantly, they were pretty unique from a drug lead point of view.. Over 75% of the compounds resembled nothing in known libraries.. And the compounds were not similar to one another.. Klein and coworkers had created a wide range of instruments other than guitars.. Of course, keeping a yeast strain alive is hardly reason to look for a new drug.. But that isn’t all these compounds can do.. At least some of these leads show excellent activity against two viruses related to BMV, Dengue and hepatitis C, and one looks particularly promising.. With a random combination of genes from a variety of biochemical pathways, yeast has been coaxed into synthesizing chemical leads that can target two medically relevant viruses.. Scientists should be able to use a similar approach to tackle other diseases.. All they need is a yeast strain with the right assay.. Yeast can make our bread rise, get us drunk, and now maybe cure us of disease.. Is there anything yeast can’t do? Well, they still can’t play a guitar.. drug discovery.. Previous Page..

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  • Title: S. cerevisiae WU-BLAST2 Search
    Descriptive info: WU-BLAST2 Search.. Datasets updated: December 6, 2011.. This form allows BLAST searches of.. sequence datasets.. To search multiple fungal sequences, go to the.. Fungal BLAST search form.. Query Comment (optional, will be added to output for your use):.. NOTE: If the input sequence is less than 30 letters you should change the default Cutoff Score value to something less than 100 or you can miss matches.. Upload Local TEXT File: FASTA, GCG, and RAW sequence formats are okay.. WORD Documents do not work unless saved as TEXT.. Type or Paste a Query Sequence : (FASTA or RAW format, or No Comments, Numbers are okay).. Choose the Appropriate BLAST Program:.. BLASTN - nucleotide query to nucleotide db.. BLASTP - protein query to protein db.. BLASTX - translated (6 frames) nucl.. query to protein db.. TBLASTX - transl.. (6 frames) nucl.. query to transl (6) nt db.. TBLASTN - protein query to translated (6 frames) nt db.. Choose one or more Sequence Datasets:.. Select or unselect multiple datasets by pressing the Control (PC) or Command (Mac) key while clicking.. Selecting a category label selects all datasets in that category.. REFERENCE (S288C) GENOMIC SEQUENCE.. Nuclear chromosomes (DNA).. Mitochondrial chromosome (DNA).. 2-micron plasmid (DNA).. GENES: PROTEIN ENCODING (S288C).. Open Reading Frames (DNA or Protein).. Genomic (Coding and Introns) Sequences of defined ORFs (DNA).. Open Reading Frames + 1000 bp Up Downstream (DNA).. GENES: ncRNA (S288C).. RNA Coding (DNA).. RNA Genomic (coding and introns) (DNA).. RNA Genomic + 1000 bp Up Downstream (DNA).. NON-GENIC SEQUENCES (S288C).. Intergenic Genomic DNA between ORFs, RNA genes, LTRs Tys (DNA).. OTHER PUBLIC SEQUENCES.. Yeast public sequences from GenBank and UniProt (DNA or  ...   or Protein).. cerevisiae strain CBS7960_cds (DNA or Protein).. PK113-7D_cds (DNA or Protein).. cerevisiae strain CLIB215_cds (DNA or Protein).. cerevisiae strain CLIB324_cds (DNA or Protein).. cerevisiae strain CLIB382_cds (DNA or Protein).. cerevisiae strain EC1118_cds (DNA or Protein).. cerevisiae strain EC9-8_cds (DNA or Protein).. cerevisiae strain FL100_cds (DNA or Protein).. cerevisiae strain FostersB_cds (DNA or Protein).. cerevisiae strain FostersO_cds (DNA or Protein).. cerevisiae strain JAY291_cds (DNA or Protein).. cerevisiae strain Kyokai7_cds (DNA or Protein).. cerevisiae strain LalvinQA23_cds (DNA or Protein).. cerevisiae strain M22_cds (DNA or Protein).. cerevisiae strain PW5_cds (DNA or Protein).. cerevisiae strain RM11-1a_cds (DNA or Protein).. cerevisiae strain Sigma1278b_cds (DNA or Protein).. cerevisiae strain T73_cds (DNA or Protein).. cerevisiae strain T7_cds (DNA or Protein).. cerevisiae strain UC5_cds (DNA or Protein).. cerevisiae strain Vin13_cds (DNA or Protein).. cerevisiae strain VL3_cds (DNA or Protein).. cerevisiae strain W303_cds (DNA or Protein).. cerevisiae strain Y10_cds (DNA or Protein).. cerevisiae strain YJM269_cds (DNA or Protein).. cerevisiae strain YJM789_cds (DNA or Protein).. cerevisiae strain YPS163_cds (DNA or Protein).. cerevisiae strain ZTW1_cds (DNA or Protein).. Options:.. For descriptions of BLAST options and parameters, refer to the.. BLAST documentation at NCBI.. Output format :.. gapped alignments.. nongapped alignments.. Comparison Matrix :.. BLOSUM62.. BLOSUM100.. PAM40.. PAM120.. PAM250.. Cutoff Score (S value) :.. default.. 30.. 50.. 70.. 90.. 110.. Word Length (W value) :.. 15.. 14.. 13.. 12.. 11.. 10.. 9.. 8.. 7.. 6.. 5.. 4.. 3.. 2.. Default = 11 for BLASTN, 3 for all others.. Expect threshold (E threshold) :.. 0.. 0001.. 01.. 1.. 100.. 1000.. Number of best alignments to show :.. 25.. 200.. 400.. 800.. Filter options :.. On.. Off.. DUST file for BLASTN, SEG filter for all others..

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  • Title: Fungal Genomes Search using WU-BLAST2
    Descriptive info: Fungal Genomes Search.. using WU-BLAST2.. This form allows BLAST searches of multiple fungal sequence datasets.. To restrict your search to S.. cerevisiae with additional BLAST search options, go to the.. BLAST search form.. Both DNA and protein datasets are available, except when noted.. With a protein sequence query, use the TBLASTN program in addition to the BLASTP program for comprehensive results, since some protein datasets are incomplete (see.. Help documentation.. ).. -------------------Saccharomyces------------------.. Saccharomyces arboricola.. Saccharomyces bayanus (DNA only).. Saccharomyces boulardii (DNA only).. Saccharomyces cerevisiae x Saccharomyces kudriavzevii.. Saccharomyces kudriavzevii.. Saccharomyces mikatae.. Saccharomyces paradoxus.. Saccharomyces pastorianus.. -------------------Candida------------------.. Candida albicans.. Candida dubliniensis.. Candida glabrata.. Candida maltosa.. Candida orthopsilosis.. Candida parapsilosis.. Candida tenuis.. Candida tropicalis.. -------------------Saccharomycetaceae------------------.. Ashbya gossypii.. Dekkera bruxellensis.. Eremothecium cymbalariae.. Kazachstania africana.. Kazachstania naganishii.. Kluyveromyces aestuarii (DNA only).. Kluyveromyces lactis.. Kluyveromyces marxianus (DNA only).. Kluyveromyces wickerhamii (DNA only).. Komagataella pastoris.. Lachancea kluyveri.. Lachancea thermotolerans.. Lachancea waltii (DNA only).. Naumovozyma castellii.. Naumovozyma dairenensis.. Ogataea parapolymorpha.. Pachysolen tannophilus (DNA only).. Saccharomycetaceae sp.. Ashbya aceri.. Tetrapisispora blattae.. Tetrapisispora phaffii.. Torulaspora delbrueckii.. Vanderwaltozyma polyspora.. Zygosaccharomyces bailii.. Zygosaccharomyces rouxii.. -------------------Other Saccharomycetales (budding yeasts)------------------.. Clavispora lusitaniae.. Cyberlindnera jadinii (DNA only).. Debaryomyces hansenii.. Lodderomyces elongisporus.. Meyerozyma guilliermondii.. Millerozyma farinosa.. Pichia kudriavzevii (DNA only).. Scheffersomyces stipitis.. Spathaspora arborariae (DNA only).. Spathaspora passalidarum.. Wickerhamomyces anomalus (DNA only).. Wickerhamomyces ciferrii.. Yarrowia lipolytica.. -------------------Schizosaccharomyces (fission yeasts)------------------.. Schizosaccharomyces cryophilus.. Schizosaccharomyces japonicus.. Schizosaccharomyces octosporus.. Schizosaccharomyces pombe.. -------------------Dothideomycetes (plant fungi)------------------.. Alternaria arborescens (DNA only).. Alternaria brassicicola (DNA only).. Aureobasidium pullulans (DNA only).. Baudoinia compniacensis.. Bipolaris maydis.. Bipolaris oryzae.. Bipolaris sorokiniana.. Bipolaris victoriae.. Bipolaris zeicola.. Hortaea werneckii (DNA only).. Hysterium pulicare (DNA only).. Lecanosticta acicola (DNA only).. Leptosphaeria maculans.. Macrophomina phaseolina.. Mycosphaerella laricina (DNA only).. Mycosphaerella pini.. Mycosphaerella sp.. Ston1.. Neofusicoccum parvum.. Parastagonospora nodorum.. Passalora fulva (DNA only).. Pseudocercospora fijiensis.. Pseudocercospora pini-densiflorae (DNA only).. Pyrenochaeta sp.. UM 256 (DNA only).. Pyrenophora seminiperda (DNA only).. Pyrenophora teres.. Pyrenophora tritici-repentis.. Rhytidhysteron rufulum (DNA only).. Setosphaeria turcica.. Shiraia sp.. slf14.. Sphaerulina musiva.. Sphaerulina populicola (DNA only).. Zymoseptoria ardabiliae (DNA only).. Zymoseptoria passerinii (DNA only).. Zymoseptoria pseudotritici (DNA only).. Zymoseptoria tritici.. -------------------Chaetothyriales (black yeasts)------------------.. Cladophialophora carrionii.. Coniosporium apollinis.. Cyphellophora europaea.. Exophiala dermatitidis.. Herpotrichiellaceae sp.. UM238 (DNA only).. -------------------Aspergillus------------------.. Aspergillus clavatus.. Aspergillus flavus.. Aspergillus fumigatus.. Aspergillus kawachii.. Aspergillus nidulans.. Aspergillus niger.. Aspergillus oryzae.. Aspergillus sojae (DNA only).. Aspergillus terreus.. -------------------Penicillium------------------.. Penicillium camemberti (DNA  ...   hamatum (DNA only).. Trichoderma longibrachiatum (DNA only).. Trichoderma reesei.. Trichoderma virens.. -------------------Sordariales (Neurospora and related)------------------.. Chaetomium globosum.. Chaetomium thermophilum.. Myceliophthora thermophila.. Neurospora crassa.. Neurospora tetrasperma.. Podospora anserina.. Sordaria macrospora.. Thielavia terrestris.. -------------------Other Sordariomycetidae (unitunicate perithecial fungi)------------------.. Gaeumannomyces graminis.. Grosmannia clavigera.. Magnaporthe oryzae.. Magnaporthe poae (DNA only).. Ophiognomonia clavigignenti-juglandacearum (Protein only).. Ophiostoma novo-ulmi (DNA only).. Togninia minima.. -------------------Other Ascomycota------------------.. Arthrobotrys oligospora.. Cerataphis brasiliensis yeast-like symbiont (DNA only).. Ceratocystis fimbriata (DNA only).. Cladonia macilenta (DNA only).. Cladonia metacorallifera (DNA only).. Dactylellina haptotyla.. Endocarpon pusillum.. Eutypa lata.. Gyalolechia flavorubescens (DNA only).. Pestalotiopsis fici.. Pneumocystis jirovecii.. Pneumocystis murina.. Saitoella complicata (DNA only).. Taphrina deformans.. Tuber melanosporum.. -------------------Agaricomycetes (gill mushrooms and related)------------------.. Agaricus bisporus.. Amanita jacksonii (DNA only).. Auricularia delicata.. Ceriporiopsis subvermispora.. Coniophora puteana.. Coprinopsis cinerea.. Dichomitus squalens.. Fibroporia radiculosa.. Fomitiporia mediterranea.. Fomitopsis pinicola.. Ganoderma lucidum (DNA only).. Gloeophyllum trabeum.. Heterobasidion irregulare.. Laccaria bicolor.. Moniliophthora perniciosa.. Moniliophthora roreri.. Omphalotus olearius (DNA only).. Phanerochaete carnosa.. Phanerochaete chrysosporium.. Phellinus noxius (DNA only).. Piriformospora indica.. Postia placenta.. Punctularia strigosozonata.. Rhizoctonia solani.. Schizophyllum commune.. Serpula lacrymans.. Stereum hirsutum.. Trametes versicolor.. Volvariella volvacea (DNA only).. Wolfiporia cocos (DNA only).. -------------------Tremellales (jelly fungi)------------------.. Cryptococcus bestiolae (DNA only).. Cryptococcus dejecticola (DNA only).. Cryptococcus flavescens (DNA only).. Cryptococcus gattii.. Cryptococcus neoformans.. Cryptococcus pinus (DNA only).. Kwoniella heveanensis (DNA only).. Kwoniella mangrovensis (DNA only).. Tremella mesenterica.. Trichosporon asahii.. -------------------Ustilaginomycotina (true smut fungi)------------------.. Malassezia globosa.. Malassezia restricta (DNA only).. Malassezia sympodialis.. Melampsora larici-populina.. Pseudozyma antarctica.. Pseudozyma aphidis.. Pseudozyma brasiliensis.. Pseudozyma flocculosa.. Pseudozyma hubeiensis.. Sporisorium reilianum.. Ustilago hordei.. Ustilago maydis.. -------------------Other Basidiomycota------------------.. Cronartium comandrae (DNA only).. Cronartium quercuum (DNA only).. Cronartium ribicola (DNA only).. Dacryopinax sp.. DJM-731 SS1.. Endocronartium harknessii (DNA only).. Microbotryum violaceum (DNA only).. Mixia osmundae.. Puccinia graminis.. Puccinia psidii (DNA only).. Puccinia striiformis (DNA only).. Puccinia triticina (DNA only).. Rhodosporidium toruloides.. Rhodotorula glutinis.. Wallemia ichthyophaga.. Wallemia sebi.. -------------------Microsporidia------------------.. Anncaliia algerae.. Edhazardia aedis.. Encephalitozoon cuniculi.. Encephalitozoon hellem.. Encephalitozoon intestinalis.. Encephalitozoon romaleae.. Enterocytozoon bieneusi.. Nematocida parisii.. Nematocida sp.. Nosema apis.. Nosema bombycis.. Nosema ceranae.. Spraguea lophii.. Trachipleistophora hominis.. Vavraia culicis.. Vittaforma corneae.. -------------------Other Fungi------------------.. Allomyces macrogynus (DNA only).. Batrachochytrium dendrobatidis.. fungal sp.. EF0021 (DNA only).. Homoloaphlyctis polyrhiza (DNA only).. Mortierella alpina (DNA only).. Mucor circinelloides.. Rhizophagus irregularis.. Rhizopus delemar.. Rhizopus microsporus (DNA only).. Rozella allomycis (DNA only).. Spizellomyces punctatus (DNA only).. Umbelopsis isabellina (DNA only).. 300.. 500..

    Original link path: /cgi-bin/blast-fungal.pl
    Open archive

  • Title: Web Primer: DNA and Purpose Entry
    Descriptive info: Web Primer: DNA and Purpose Entry.. Web Primer redesign survey.. Share your opinions so the new tool meets your needs.. Sequences of.. primer sets.. available to the community.. DNA Source.. [info].. Locus.. : Enter a standard gene name or systematic ORF name (i.. e.. ACT1, YKR054C).. OR.. Enter the DNA Sequence (numbers are OK, but comments should be removed).. Purpose: PCR or Sequencing.. PCR.. or.. SEQUENCING..

    Original link path: /cgi-bin/web-primer
    Open archive



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