CORNELL FACILITIES

• E-SHOP

• DNA SEQUENCING FACILITY

  • HOW TO READ A SEQUENCE CHROMATOGRAM

  • SNAPGENE (VIEW CHROMATOGRAMS)

  • SOFTWARE FOR CHROMATOGRAM VIEWING (4PEAKS)

  • SOFTWARE FOR CHROMATOGRAM VIEWING AND SEQUENCE ALIGNMENT (APE)

• PROTEOMICS CORE

• TREx FACILITY (RNASEQ)

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DATABASES & WEB SERVERS

   GENERAL TOOLS & DATABASES:

• PUBMED

• GOOGLE SCHOLAR

• UNIPROT (PROTEIN SEQ & FUNCTIONAL INFO)

• G:PROFILER (CONVERT GENE OR PROTEIN IDS)

• BLAST (BASIC LOCAL ALIGNMENT TOOLS)

• DIOPT (ORTHOLOG FINDER)

• BIOPLEX (PROTEIN COMPLEXES)

• SITES WITH LISTINGS FOR MULTIPLE DATABASES & WEB SERVERS:

  • ALLIANCE MINE (SEARCH GENES, PROTEINS, PATHWAYS, PHENOTYPES, LITERATURE)

  • BIP SERVER (COLLECTION OF DATABASES & ANALYSIS PROGRAMS)

  • DATABASE COMMONS (REGISTRY OF DATA REPOSITORIES)

  • EMBL EUROPLEAN BIOINFORMATICS INSTITUTE (SEQUENCE ANALYSIS TOOLS

  • EXPASY (SWISS BIOINFORMATICS RESEARCH PORTAL)

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   YEAST DATABASES:

• SACCHAROMYCES GENOME DATABASE (SGD)

• PRIMERS-4-YEAST (SCHULDINER LAB)

• YEAST RESOURCE CENTER

• THE CELL MAP

• FITDB

• YEAST MINE (NOW PART OF ALLIANCE MINE DATABASE)

• LOQATE (PROTEIN LOCALIZATION)

• SCPD (PROMOTER DATABASE)

• YEASTRACT (TF BINDING SITES)

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   SEQUENCE ALIGNMENT TOOLS:

• SEQUENCE ALIGNMENT SOFTWARE (WIKI LISTING)

• CLUSTAL OMEGA (SEQUENCE ALIGNMENT)

• CLUSTALW (SEQUENCE ALIGNMENT)

• ESPRIPT 3.0 (ALIGNMENTS + SECONDARY STRUCTURE INFO.)

• MULTIPLE ALIGN SHOW (USE WITH CLUSTAL ALIGNMENTS)

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   PROTEIN STRUCTURE & STRUCTURE PREDICTION TOOLS & DATABASES:

• PROTEIN DATA BANK (PDB)

• PROTEIN HOMOLOGY SEARCH:

  • HMMER (HOMOLOGY SEARCH)

  • SMART (PROTEIN DOMAINS)

• SECONDARY STRUCTURE:

  • PSIPRED

  • DISPROT (PROTEIN DISORDER)

• TERTIARY STRUCTURE PREDICTION:

  • ALPHAFOLD

  • ​HHPRED

  • PHYRE2 (PROTEIN FOLD RECOGNITION)

  • RAPTOR

  • trROSETTA

• COACH-D (PROTEIN-LIGAND BINDING SITE PREDICTION)

• PHOBIUS (COMBINED TOPOLOGY AND SIGNAL PEPTIDE PREDICTOR)

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  GENOME-FOCUSED DATABASES:

• GWIPS (GENOME BROWSER)

• COEXPRESSdb (CO-REGULATION GENE RELATIONSHIPS)

• CLADE-O-SCOPE (CO-EVOLUTION GENE RELATIONSHIPS)

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   REDOX-FOCUSED DATABASES:

• DSDBASE (DISULFIDE DATABASE)

• CYSMODDB

• iCYSMOD

• METOSITE

• OXIAGE

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   LIPID-RELATED DATABASES:

• LIPID DROPLET KNOWLEDGE PORTAL

• CRISPRLIPID (GENOMIC SCREENS RELATING TO LIPID DROPLETS)

YEAST RESOURCES

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• INTRODUCTION TO YEAST GENETICS AND MOLECULAR BIOLOGY

• FRED SHERMAN'S GETTING STARTED WITH YEAST

• COMMON LAB SACCHAROMYCES CEREVISIAE STRAIN INFO (S288C, W303, ETC)

• HORIZON (YEAST STRAIN & ORF COLLECTIONS INFO)

• COMMON SACCHAROMYCES CEREVISIAE AUXOTROPHIC MARKER MUTATIONS

• CORA STYLE'S YEAST IDIOSYNCRASIES

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MOLECULAR BIOLOGY RESOURCES

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   GENERAL CLONING-RELATED MANUALS:

• GUIDE TO MOLECULAR CLONING (ADDGENE)

• PLASMIDS 101 (ADDGENE) (INFO ABOUT CLONING, EPITOPE TAGS, STRAINS, ETC)

• CRISPR 101 (ADDGENE)

• QIAGEN MINIPREP HANDBOOK

• QIAGEN QIAQUICK HANDBOOK

   BACTERIAL STRAIN INFO:

• COMMON LAB BACTERIA GENOTYPES (FOCUSED ON STRAINS FOR CLONING)

   SITE-DIRECTED MUTAGENESIS (QUIKCHANGE) MANUALS:

• AGILENT QUIKCHANGE MANUAL (BASIS FOR LAB QC PROTOCOL)

• AGILENT QUIKCHANGE MULTI MANUAL (BASIS FOR LAB MULTI-QC PROTOCOL)

• AGILENT QUIKCHANGE MULTI LIGHTNING MANUAL (PURCHASED KIT)

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   OLIGO-DESIGN WEBSITES FOR QUIKCHANGE MUTAGENESIS:

• QUIKCHANGE OLIGO DESIGN WEBSITE

• QUIKCHANGE PRIMER MELTING TEMPERATURE CALCULATOR

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   NEW ENGLAND BIOLABS STUFF:

• NEB RESTRICTION ENZYME BUFFER CHART (OLD BUFFER SYSTEM)

• NEB RESTRICTION ENZYME BUFFER CHART (NEW BUFFER SYSTEM)

• INTERACTIVE DOUBLE DIGEST BUFFER FINDER (NEW BUFFER SYSTEM)

• INTERACTIVE ENZYME FINDER

• HOW WELL DOES YOUR RESTRICTION ENZYME CUT AT DNA ENDS ?

• ISOSCHIZOMERS

• COMPATIBLE COHESIVE ENDS

• PHUSION ENZYME

• TAQ ENZYME

• 1 KB DNA LADDER

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BIOCHEMISTRY RESOURCES

   PROTEIN-EXPRESSION PLASMID INFO:

• pET E. COLI T7 EXPRESSION VECTORS

• NOVAGEN pET MANUAL

• pGEX E. COLI EXPRESSION VECTORS

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   BACTERIAL STRAINS (FOR PROTEIN EXPRESSION) INFO:

• BACTERIAL STRAINS FOR PROTEIN EXPRESSION (ADDGENE LIST - ALSO LISTS BACKGROUND INFO.)

• BACTERIAL STRAINS FOR PROTEIN EXPRESSION (WOLFSON CENTER LIST)

   GE HEALTHCARE (CYTIVA) PROTEIN PURIFICATION HANDBOOKS:

• DOWNLOAD LINK (2022 VERSIONS)

 

   BUFFER TABLES:

• BUFFER TABLES

• pH VERSUS TEMPERATURE FOR TRIS (A GUIDELINE - CHECK ACTUAL pH WITH METER)

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   DETERGENT INFORMATION:

• CALBIOCHEM'S DETERGENT BOOK I

• CALBIOCHEM'S DETERGENT BOOK II

 

   PROTEIN INHIBITOR INFORMATION (INCLUDING PROTEASE INHIBITORS) :

• ROCHE PROTEASE INHIBITORS HANDBOOK

• CALBIOCHEM'S INHIBITORS HANDBOOK

   THERMO SCIENTIFIC PIERCE TECHNICAL HANDBOOKS:

• DIALYSIS, DESALTING, DETERGENT REMOVAL

• PROTEIN ASSAYS (INCLUDES COMPATIBILITY TABLE)

• AVIDIN-BIOTIN TECHNICAL HANDBOOK

• METHODS TO MONITOR PROTEIN INTERACTIONS

   ADDITIONAL HANDBOOKS / TABLES:

• QIAGEN NI-NTA HANDBOOK

• ANTIBODY COMPATIBILITY WITH PROTEIN A / PROTEIN G

• ANTIBODIES 101

• FLUORESCENT PROTEINS 101

GENERAL LAB RESOURCES

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• ROTOR RPM <-> RCF CONVERSION

• CHEMICAL RESISTANCE OF PLASTICS (CAN I PUT THAT SOLVENT INTO MY PLASTIC TUBE)

• LAB MATH (MAKING SOLUTIONS)

• WILEY CURRENT PROTOCOLS

• MOLECULAR PROBES HANDBOOK

• SOME BASICS ON HOW TO KEEP A LAB NOTEBOOK