Fungal genome resources at NCBI

Abstract

The National Center for Biotechnology Information (NCBI) is well known for the nucleotide sequence archive, GenBank and sequence analysis tool BLAST. However, NCBI integrates many types of biomolecular data from variety of sources and makes it available to the scientific community as interactive web resources as well as organized releases of bulk data. These tools are available to explore and compare fungal genomes. Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries. Some tools though are resources specific and can be indirectly accessed from a particular database in the Entrez system. These include graphical viewers and comparative analysis tools such as TaxPlot, TaxMap and UniGene DDD (found via UniGene Homepage). Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI. Depending on the focus and goal of research projects or the level of interest, a user would select a particular route for accessing genomic databases and resources. This review article describes methods of accessing fungal genome data and provides examples that illustrate the use of analysis tools.

Figure 1

Screenshots showing a section of an alignment created by MUSCLE with matched conserved domains and a neighbor-joining tree of the fungal RPB1 protein cluster as displayed in the Genome Workbench application.

Figure 2

(A) A TaxMap of chromosome 8 of Aspergillus fumigatus showing the taxonomic distribution of best hits (Eukaryotes = pink; Bacteria = blue) with (B) a list of best hits to bacteria produced by the link (number 5) in the Best column.

Figure 3

(A) Pre-computed BLAST results of the Aspergillus fumigatus gene with the highest similarity score in the list of 5 best hits to Bacteria (see Fig. 1). (B) A BLink report of the top bacterial hit as query (RefSeq accession YP_555549) and the results filtered to show only Fungi hits.

Figure 4

The Entrez Gene page of the steroid monooxygenase gene from Aspergillus fumigatus (locus tag AFUA_8G00440), showing gene related information including the sequence viewer and a link (Open Full View) to see the full view.

Figure 5

(A) The default view after following the sequence viewer link from the Entrez Gene page of locus AFUA_8G00440. (B) A graphical view of the genome neighbourhood around locus AFUA_8G00440 after modifying settings in the default view displayed above.

Figure 6

Results of a global Entrez search using the following as query, “polyketide synthase” AND Bacteria AND Fungi.

Figure 7

(A) A ranked list of biosystems weighted by the frequency of proteins present in the GI input list obtained from the BLAST results in Fig 2A. (B) A ranked list of PubMed records associated with the best BLAST hits in Fig 2A.