Fly-Specific Tools and Databases
- eCIS-ANALYST
- eCIS-ANALYST searches the Drosophila melanogaster and Drosophila pseudoobscura genomes for conserved clusters of transcription-factor binding sites.
- Target Explorer
- Software for identification of new target genes for transcription factors in the Drosophila genome
- Assembly/Annotation/Annotation
- Hosts sequences, assemblies, annotations and analyses of 12 related Drosophila species.
- FlyMine
- An integrated database for Drosophila and Anopheles genomics
- Flynet Server
- Build networks from Drospophila protein-protein interactions detected experimentally or mapped cross-species from Saccharomyces orthologs.
- FLIGHT Database
- FLIGHT is a database designed to integrate data from high-throughput experiments carried out in Drosophila cell culture.
- Homophila
- A human disease to Drosophila gene databse.
Worm-Specific Tools
- Worm Motif Lexicon
- Finds single motifs in C. elegans genome and provides quick links to NCBI files of genes nearest the motifs.
Plant-Specific Tools
- Arabidopsis Pattern Match
- Pattern Match allows you to search for any short (<20 residues) nucleotide or peptide sequences, or ambiguous/degenerate patterns. It uses the same Arabidopsis dataset as TAIR's BLAST and FASTA programs.
Universal Tools and Databases
- Cister
- Cis-element Cluster Finder. This web tool enables you to search for clusters of your favorite binding sites in your favorite stretch of DNA (upto 100 kb).
- DNA Duster
- This program removes formatting characters and other non-sequence related stuff from a sequence. It outputs in a variety of formats such as Fasta.
- GenePalette
- Genepalette is a desktop application that converts large and small NCBI gene annotation files into colorful graphical representations of intron/exon structure. The program allows you to locate and label binding sites, regulatory motifs, restriction enzymes, SNPs, etc.
- Genscan
- This server provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.
- MEME
- MEME is a tool for discovering motifs in a group of related DNA or protein sequences. A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences.
- MatInspector
- A software tool that utilizes a large library of matrix descriptions for transcription factor binding sites to locate matches in DNA sequences.
- TESS
- TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, IMD, and CBIL-GibbsMat databases.