As of October 2008, Fourmidable contains nucleotide sequence data for the fire ant S. invicta
and the black garden ant L. niger
as well as gene expression data for S. invicta
. Currently accessible data are summarized in Table . Sequencing, gene expression profiling, and genotyping data are rapidly expanding and will be added as they become publicly available. Fourmidable's home page [27
] centralizes links and search facilities to access Fourmidable's data and tools.
There are several manners of accessing sequence information in Fourmidable. First, single sequences can be searched by species as well as by partial identifiers for input sequences or assembled contigs. Second, lists of identifiers can be used for searching. Third, user-supplied sequence data can be used for BLAST similarity searches against sequences in Fourmidable. Finally, users can navigate inferred Gene Ontology annotations for biological processes, cellular components, and molecular functions using the AmiGO browser [28
]. The first two search manners result in tables as described below. BLAST searching and GO browsing produce lists of sequence identifiers that can be used as inputs for the first two search manners.
Sequence searches result in tables with one line per sequence for easy access to sequence annotation (see Figure ). In particular:
Figure 1 Table of sequence search results. For each result, the following are shown from left to right if applicable: sequence identifiers for raw and assembled sequence (these respectively link to the raw datafiles and assembly information); links to raw and (more ...)
- Clicking on an identifier in the "Raw Sequence" column provides information on how that sequence was obtained and allows users to download the raw sequence. Tracefiles can be viewed with the Baylor College of Medicine Trace Viewer [29
] or downloaded.
- Cleaned FASTA-format sequence can be downloaded for individual singlets and contigs.
- If the sequence is part of an assembled contig, the "Assembled Contig" identifier links to a display of the consensus sequence and the relevant input sequences as well as their quality scores. Additionally, a multiple sequence alignment highlights nucleotide polymorphisms within the consensus sequence.
- BLAST results between the sequence of interest and sequences from the non-redundant protein database and several insect nucleotide and protein databases are summarized by blue and red buttons, indicating weak (0.01 > E-value > 10-5) and stronger similarity (E-value ≤ 10-5) respectively. Clicking on a button displays the complete BLAST report.
- An additional link to Interproscan results and six-frame protein translations is displayed if Interproscan annotation is available.
A convenient repository is available for ant molecular biology protocols (commonly in .doc or .pdf formats). New or revised protocols can be added via an upload form. Fourmidable also supports upload of result files from microarray gene expression experiments. The GEDAI platform allows straightforward sharing of microarray results and performing simple microarray analyses (including preprocessing, direct and indirect two-sample comparisons, 2 × 2 factorial and gene set enrichment analyses). GEDAI also provides summaries of the expression levels of specific microarray probe identifiers across multiple microarray experiments. Finally, Fourmidable provides download links to individual files containing all raw or assembled sequences, as well as sequence annotation in text format [see also Additional file 4
The sequence assembly and annotation information provided by Fourmidable has already proved useful in several published studies [14
]. Most recently, Fourmidable's data helped J. Wang and colleagues to characterize genes that are differently expressed between workers from two alternative social forms of fire ants [6
Fourmidable was initially developed as a private database in Lausanne. Recently it has been updated and made publicly accessible because of increasing interest in ant molecular research. To further develop Fourmidable, several primary investigators in the USA have submitted grant applications. This should lead to improved integration of gene expression data with sequence annotation, as well as support for genetic mapping and linkage data. When large amounts of genomic sequence become available for ants, the current approach for assembly and annotation may become computationally unrealistic. An alternative may be to adapt existing genome assembly, annotation and browsing tools.