Contents:

Overview

The AspGD site map provides a comprehensive listing of major AspGD resources and tools. It is organized by the major categories available at AspGD, which correspond to the links located on the left side of the home page. The resources and tools available in that category are listed, followed by a description of the resource and its primary use. A link to the help documentation is also provided, if it is available for that resource.

For more information on how to navigate around AspGD, please read the Getting Started page.

Site map

Category Resource Description Primary Use Help Page
Search Options Quick Search and Text Search Search the AspGD relational database, including literature guide, colleague information, protein information, and text. Search AspGD database using keywords.
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Advanced Search Find a chromosomal feature (e.g. gene, ORF, centromere) based on selected criteria (e.g., chromosome number, GO-Slim terms, etc.) Find chromosomal features that match specific properties or annotations.
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Search AspGD Web Pages Search AspGD HTML pages, excludes the relational database. Find AspGD web pages using keywords located on the page.
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Expanded Phenotype Search Search the text of all phenotype information to find phenotypes of interest and view the genes associated with them. Search for keywords related to a phenotype (e.g., "conidiation"), an allele (such as veA1), or an experimental condition (e.g., "light").
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Category Resource Description Primary Use Help Page
Help Resources Getting Started Common uses of AspGD for the first time user. Get a brief overview of navigating around AspGD.  
FAQ Answers to some common questions asked about AspGD. Get an answer to a commonly asked question.  
What's New in AspGD Changes and additions to AspGD resources. Find new resources at AspGD and when they were added.  
SGD's Glossary List of terms and definitions at SGD. Find the definition of a new term.  
Category Resource Description Primary Use Help Page
Analysis & Tools BLAST Search Aspergillus DNA and protein sequence datasets for similarities to a particular sequence. Find similarities between a sequence of interest and Aspergillus DNA or protein sequences.
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Sybil: Comparative Genomics Tool Sybil, a web-based tool for comparative genomics analysis implemented by the Broad Institute. Search orthologous genes among sequenced Aspergillus species.
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Gene/Sequence Resources Retrieve Aspergillus genomic sequence from AspGD or enter a DNA or protein sequence to analyze using numerous AspGD resources. Display or analyze an Aspergillus sequence (or other sequence) in many ways.
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GBrowse Genome Browser
A. nidulans GBrowse
A. fumigatus GBrowse
A. niger GBrowse
A. oryzae GBrowse		 GBrowse allows viewing and navigation of genomic sequence. The GBrowse tool is part of the Generic Model Organism Database Project. Navigate the chromosomes set. View nucleotide and protein sequence.
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Pattern Matching A pattern matching program that allows ambiguous matches but not gaps. Find short DNA/protein sequence matches in Aspergillus genomes.
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Design Primers Recommends primers appropriate for either PCR or sequencing of a given gene or DNA sequence, within parameters set by the user (end points, Tm, GC/AT ratios, etc.). Design sequencing and PCR primers for Aspergillus or other input sequences.
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Genome Restriction Analysis Generates a restriction map of a specified DNA sequence. The restriction map may include all enzymes, or a subset of enzyme types (3' overhangs, 5' overhangs, blunt ends, or enzymes that cut once or twice). Display the restriction map for an Aspergillus or other input sequence.
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SGD's Fungal BLAST Search multiple fungal genomes, including Aspergillus genomes, for similarity to a particular sequence. Find similarities between a sequence of interest and fungal nucleotide or protein sequences.
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Category Resource Description Primary Use Help Page
GO Resources What is GO? SGD help page that explains the philosophy of GO. Get an overview of Gene Ontology (GO).  
SGD's GO Tutorial Tutorial that highlights pages and tools that use GO annotations to familiarize users with the Gene Ontology (GO). Learn where GO annotations are located on AspGD pages and how to use them.  
GO Slim Mapper GO Slim is a set of GO terms that represent major sections of the ontology. Gene products are annotated to the most specific GO term possible. This tool traces the specific annotations to their broader GO Slim terms for a given set of Aspergillus genes. Map a set of Aspergillus genes to broad GO Slim categories.
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GO Term Finder Aspergillus gene products are annotated to the most specific GO terms possible. Common parent terms may not be obvious. This tool determines the GO terms that a set of genes share in common and graphically displays the significant lineage. Find GO terms that are shared by a group of Aspergillus genes.
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Category Resource Description Primary Use Help Page
Community Info Conferences & Courses Link to a list of conferences & courses. Find an upcoming conference.  
Community News Links to Aspergillus news postings. Find out about items of interest to the research community.  
Aspergillus Laboratories Links to laboratories who have submitted colleague information to AspGD. Find a PI (principal investigator) of a Aspergillus laboratory.  
Aspergillus Community Job Postings Announcements of employment opportunities that are related to Aspergillus biology. View job openings.  
External Links List of useful external sites Find a web site for information not available at AspGD.  
Category Resource Description Primary Use Help Page
Submit Data
Gene Naming Guidelines Guidelines for choosing and registering a gene name as agreed upon by the members of the Aspergillus research community. Find information about registering a gene name and determining when the gene name becomes a standard name.  
Colleague Submission/Update Form Form to submit colleague information to AspGD. Your information will be available to AspGD users. Add or update your information in AspGD.
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Contact AspGD Form to submit suggestions or questions to AspGD. Send suggestions or questions to AspGD.  
Category Resource Description Primary Use Help Page
Download Data Batch Download Tool that allows simultaneous retrieval of DNA sequences, protein sequences, and chromosomal coordinate information for a list of Standard gene names or Feature names. Download information for a list of genes from AspGD.
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Gene Ontology (GO) Annotations File The gene_association.aspgd file contains the Gene Ontology (GO) curation from AspGD. Download tab-delimited files of GO information from AspGD.
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Chromosomal Feature File Tab-delimited file of information about current chromosomal features in AspGD. Download feature (gene) names, aliases, descriptions, and other information from AspGD.
Phenotype Annotations File Tab-delimited file containing all of the mutant phenotype annotations in AspGD Download all current mutant phenotype information from AspGD.
Sequence Files The sequence download directory contains sequence from Aspergillus chromosome sequencing projects, and derivatives thereof. Download current or archived sequence data.
Orthologs and Best Hits This directory contains mappings of orthologs and BLAST Best Hits among Aspergillus genes, and orthologs or BLAST Best Hits between Aspergillus and S. cerevisiae genes, plus additional associated information. Download homolog data.
Aspergillus GO Slim Annotations File The GOslim_gene_association.aspgd file contains GO Slim annotations for Aspergillus genes, using the AspGD GO Slim instead of the entire Gene Ontology. Download tab-delimited files of GO information from AspGD.
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Category Resource Description Primary Use Help Page
About AspGD About AspGD About the AspGD project. Find out background information on the AspGD project.  
AspGD Genome Snapshot
A. nidulans
A. fumigatus
A. niger
A. oryzae		 Annotation statistics, updated daily. Find information about the characterization of the genomes in AspGD.
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Citing AspGD How to cite AspGD in publications. References to use in citing AspGD.  
Staff Names and addresses and AspGD staff. Find out who works at AspGD.  

A complete list of genes may be found here.

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