Getting Started with The Aspergillus Genome Database


This page presents answers to some basic questions that new users might ask about AspGD. An overview of information about the AspGD website can be found on the Help Resources page.
Contents:

Aspergillus nidulans vs. Emericella nidulans

Both Aspergillus nidulans and Emericella nidulans refer to the same species, at different stages of its life cycle. Aspergillus nidulans is an "imperfect" stage (anamorph) that reproduces asexually through conidia, whereas Emericella nidulans is a sexually reproducing stage (teleomorph) that produces fruiting bodies, cleistothecia, containing asci with ascospores. Currently, the name Aspergillus nidulans is predominantly used to refer to this species.


What types of information does AspGD contain?

AspGD is an organized collection of genetic and molecular biological information about filamentous fungi of the genus Aspergillus. AspGD contains information about genes and proteins from Aspergillus nidulans (Emericella nidulans) and Aspergillus fumigatus genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. The AspGD Home page is the main entry point for the database; it contains a sidebar with links to AspGD resources.

AspGD is aimed at scientists. AspGD curators cannot answer medical or health-related questions.


How is AspGD organized?

An overview of the content and organization of AspGD is presented in the sitemap.

The basic unit of AspGD is the Locus Summary page (for an example, see A> nidulans VeA). Each gene has an individual Locus Summary page. Genetic loci that are not tied to a DNA sequence also have Locus Summary pages. The Locus Summary page is linked to the orthologs and best hits in the other Aspergillus species and Saccharomyces cerevisiae, enabline navigation between groups of orthologs of multiple different species. All information relevant to a particular locus is either presented on or linked to the Locus Summary page. Tools for analysis and comparison of the locus are also accessible from the Locus Summary page.

Locus Summary pages are accessible by using the Search Options form or by using the "Quick Search" box at the top of any AspGD Locus Summary or tool page. In addition, gene or protein names appearing anywhere in AspGD are hyperlinked to the corresponding Locus Summary page.

Many additional AspGD pages, including tools, documentation, data submission forms, and others, are accessible from the AspGD Home page.


How do I find information about an Aspergillus gene or protein of interest?

If you know the genetic or systematic name of the gene you are interested in, entering it in either the Quick Search box at the top of most AspGD pages or in the Search Options form will bring you to that Locus Summary (or to a list of genes, if the same name has been used for two or more genes, for example, orthologs that share the same gene name).

What about gene names, aliases and identifier formats? For A. nidulans, the ANxxxx identifier is used as the primary systematic name in AspGD. The ANID_xxxxx identifiers created by the Broad Institute and the CADRE ANIA_xxxxx identifiers have been added as gene aliases for A. nidulans gene names. Names with appended decimals such as ANxxxx.3 or ANID_xxxxx.1 are accepted in the Quick Search Text Box however, appended decimals are not accepted as gene input for tools such as GO Slim Mapper, GO Term GO Term Finder, Gene/Sequence Resources, and Restriction Analysis.

Sometimes you may need to investigate genes or proteins without knowing their names. You can search for a class of similarly named genes using the wildcard character (e.g., searching for 'lre*' brings up LreA and LreB). Or, you can search with the name of a protein (e.g., actin) or protein complex (e.g., cytochrome c oxidase), or a Gene Ontology (GO) term (see the GO section) to bring up lists of the Locus Summary pages where this text occurs. Each gene name in the hit list resulting from the search is hyperlinked to the corresponding Locus Summary.

The Locus Summary is the central clearinghouse for all information specific to that gene and tools for its analysis, including:


How do I find groups of genes or proteins that share a function, role, or location within the cell?

Gene products in AspGD are classified according to the Gene Ontology (GO) system of classification. Gene products are assigned GO terms that describe their molecular functions and subcellular locations, and the biological processes in which they are involved. The terms may be searched to find the set of proteins that have been annotated to a particular term. A detailed explanation of the GO system and how to use and search it is presented in a GO tutorial provided by the Saccharomyces Genome Database (SGD).


How can AspGD help me interpret the results of large-scale experiments?

Lists of Aspergillus nidulans open reading frames and their characteristics are essential for keeping track of the results of any large-scale experiment. A variety of different tab-delimited text files containing data collected by AspGD, listed on the Data Download index page, are freely available for downloading.

Interpreting the results of functional genomics experiments that identify large groups of genes with something in common (e.g., transcriptional coregulation, similar null phenotypes, etc.) presents a special challenge in integrating what is known about each gene to find the significance of the trends observed. Two tools at AspGD facilitate such analysis. The GO Slim Mapper takes a list of genes and displays how many are annotated to each of the parent GO Slim terms, allowing visualization of the distribution of the input gene set over broad biological processes, biochemical functions, or subcellular localizations. The GO Term Finder tool also takes a list of genes as input, and identifies GO terms shared among members of the group. The difference between the two tools is that the GO Slim Term Mapper maps genes to broad parent GO terms, while the Term Finder identifies specific, granular terms shared by the group. The SGD GO tutorial provides details on the use of these tools.


How do I view orthologous genes from multiple Aspergillusspecies?

The "View ortholog cluster" link next to the "Orthologous genes in Aspergillusspecies" section allows you to view ortholog and synteny information among multiple Aspergilli. The ortholog and synteny information is viewed with the Sybil viewer.


What information does the Genome Snapshot/Overview Page provide?

The Genome Snapshot/Overview provides daily-updated information on the annotation status of the various Aspergillus genomes. Each genome is displayed on its own page (for example, A. nidulans Genome Snapshot, or A. fumigatus Genome Snapshot). The data included on these pages are:

How can AspGD help me design experiments using Aspergillus genes?

The Gene/Sequence Resources page presents a versatile array of tools allowing retrieval and analysis of any portion of the Aspergillus genomes in AspGD, or analysis of your own input sequence. Sequences may be retrieved from a specific region of the genome, given a genetic or systematic name, and may include sequence upstream and/or downstream of the region if desired. Alternatively, chromosomal coordinates may be specified to retrieve part or all of a chromosome. Finally, the user may start with his/her own input sequence. Once a sequence is retrieved or entered, tools allow its analysis in multiple different ways, including translation, restriction mapping, BLAST and FASTA analysis, and primer design. The user may select a desired format (GCG, FASTA, etc.) for the output of many of the tools. The oligonucleotide primer design and BLAST analysis tools are also available as direct links from the toolbar at the top of many AspGD pages.

Additional tools and resources that facilitate sequence analysis and cloning may be accessed from the Search Options index page They include an assortment of search tools, including the Pattern Matching tool, which finds short sequences or sequence patterns in nucleotide or protein sequences.


How can I download data in bulk for use in a spreadsheet or other form?

All of AspGD's data are freely available to the public for download. The AspGD curators are available to assist researchers by creating custom files containing particular data of interest.


How can AspGD help me participate in the Aspergillus nidulans research community?

Several different kinds of information for the Aspergillus research community are available through AspGD. You can add your contact information to AspGD's directory of colleagues, which can be searched by last name. You can also search or browse a list of Aspergillus research laboratories. AspGD also maintains a list of upcoming conferences.


How can I find out what's new in AspGD?

Current information about AspGD is displayed on the AspGD Home page. Additional community information is found on the Aspergillus Community News page.


How can I get more help?

All AspGD help resources are listed on the Help Resources page. The 'Help' button in the upper right corner of each tool and Locus Summary page is linked directly to help documentation for that particular page.

For more general questions, the Frequently Asked Questions page is a good place to start. It includes common questions about AspGD.

The Saccharomyces Genome Database (SGD) Glossary page lists definitions of genetic, bioinformatic, and other terms used in SGD and in AspGD.

A tutorial, provided by SGD, is available to illustrate the use of the GO tools.

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