The Forsburg Lab pombe Pages:
Links for sequence analysis

• NCBI
• NIH model organisms page
• Saccharomyces Genome Database
• GeneDB, a friendly front end to the pombe data from the Sanger
• Tutorial on Pfam from the Sanger
• Chlamydomonas genome site. aka "green yeast"
• Genomics page from Wiley publishing includes genomics community links
• TIGR
• Science Functional Genomics from Science Magazine
• Proteome, for YPD and pombePD
• Genecards for human genes, includes lists of orthologues
• Review of sequence gazing from Nature Genetics
• GOLD: Genomes OnLine Database
• vector DB at Stanford, has vector sequences.

• BLAST both yeast genomes at once (NCBI)
• NCBI BLAST
• Blitz search
• WUSTL Blast archive
• Organism specific search engines
• SRS-FASTA
• pombe Blast server (UK)
• S. pombe cDNA blast server (Japan)
• Saccharomyces Blast server
• C. elegans blast server 1 and 2, from the Sanger Institute, or from WUSTL
• Yeast blast from NCBI
• consensus sequence zen

• Searching genbank
• database mining tools from NCBI
• Research tools from SDSC
• MAST, useful for distant homologues
• DART: 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.
• Expasy
• Pedro's Research Tools
• Expasy proteomics tools
• Bioinformatics accelerator list (at Stanford)
• MBCR database links
• BCM search launcher
• protein structure prediction
• WUSTL sequence center
• seq retrievel service
• comp biol at NIH (links and tools)
• Gene Ontology Consortium for functional categories
• Expasy proteomics tools list
• How to read a sequence logo
• how to make a sequence logo (download and compile)
• how to make a sequence logo (webserver)

• SMART database at EMBL. Start here for domains!
• String database at EMBL, summarizes interactions.
• Conserved domain databasePawson Lab Domains Database
• Pfam from 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 Rio. 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 this tutorial on PFAM from the Sanger.
• Conserved domain database
• Blocks including Blocksearcher and Blockmaker
• Scan site from MIT.
• Prosite
• SCOP allows structural classification
• Nuclear localization sequence server; also see this list of known NLSes
• Pestfind, to locate PEST sequences
• Multiple alignment server
• boxshade server
• Multi align
• Regulatory Sequence Analysis Tools (RSAT) website provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.
• Phylip allows you to build trees (dendrograms) from alignment data

• PP search
• XREF-DB (model organisms vs. human disease genes)
• NCBI search page
• Database map (BRITE)
• Gene coversion table for pombe and cerevisiae genes.

• Sanger Sequence Database
• Start here: GeneDB provides visually friendly access to the curated dataset.
• Genome statistics
• The Sanger Institute pombe genome sequencing project.
• Using the GO terminology to access the pombe genome sequencing project through Amigo
• Map viewer from NCBI. This is a great site that provides graphic clone maps and genetic and chromosome maps.
• Pfam identifies protein family motifs
• Predicted function using Amigo. Also for functional classification searches. Categories agree with the Gene Ontology Consortium.
• Gene name or keyword search through GeneDB. This is the best way to find your gene or class of interest. Use this Boolean query tool for more advanced searches of GeneDB.
• View cosmids with Artemis tool
• Protein motif search
• eMowse will search the chosen protein sequence database with protein fragment information and return the protein(s) which most likely correspond to your peptide data
• Species distribution of domains: Go to the Pfam webpage, choose the 'BROWSE PFAM' option, select a domain, and then ask to see the species distribution
• Chromosome I status and cosmids
• Chromosome II status and cosmids
• Chromosome III status and cosmids
• Functional genomics at the Sanger Institute--DNA microarrays!

• Check out the recently released S. japonicus sequence

• Expression
• Gene Expression Viewer from Jurg Bahler, which contains the data from meiotic, cell cycle, and stress expression expts.
• Microarrays at SUNY available to the community
• S. pombe epigenome page from Shiv Grewal
• ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Intron_Data/
• manual map of UTRs on genome sequence
• S. pombe is now included in the Regulatory Sequence Analysis Tools (RSAT) website. This site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences.
• Primer design Web-interface scripts that automatically design primers for PCR-based gene targeting. (Click link for "software"). 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.
• How to delete a pombe gene in 8 days will design primers for any ORF

• Other sites
• NIH S. pombe page: The Trans-NIH S. pombe initiative.
• FYSSION: pombe strain resources at Sussex.
• Yeast Genetic Resource Center Japan. : pombe strain resources in Japan.
• Transposon sequences in pombe includes coordinates of LTRs and LTR fragments
• This online program predicts introns and exons.
• GFP fusion library images of intracellular localisations are now available on the web at http://www-karc.crl.go.jp/bio/CellMagic/index.html
• Also see the S. pombe post genome database with results from a systematic analysis of protein expression and localization.
• Pedent automated protein analysis of S. pombe at MIPS.
• The NIH Genobase pombe gene list, for known genes
• Swiss Prot pombe entries
• PIR search for pombe proteins
• download all current pombe entries in Genbank
• tRNA scan analysis of S. pombe genome
• DNA structural analysis
• Proteome analysis at EBI
• Gene conversion table lists budding yeast homologues of (some) fission yeast genes.
• Restriction site usage in pombe genome
• codon usage in S. pombe
• TAP tagging resources:
  Gould lab TAP-tag page
  • Juraj Gregan's Tap Tagging any ORF in pombe page

• Pombe community news
• Pombeweb : homepages and more
• Whitepaper from the Broad Institute on sequencing other Schizosaccharomyces sp.

• genequiz from the EBI gives access to functional data across genomes--helps you find out what your protein does based on comparisons to many complete genomes.
• GRID: 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.
  A project to record published fission yeast genetic and physical interactions is underway with Mike Tyers and the GRID group at Toronto. A sample page is here. 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 val (AT) SANGER (DOT) A C (DOT) U K to join the pombe GRID mailing list.
• Meta analysis of coexpression data from 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 Science paper which you can search for your favorite genes.

• Yale Genome resources
• Yeast resource Center for protein analysis (microscopy, 2 hybrid, mass spec)
• Saccharomyces Genome Database

• Sequence Analysis Software
• OSprey is a viewer for protein interaction data
• Biological Software Resources

© S. L. Forsburg .