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• coderet - Extract CDS, mRNA and translations from feature tables (part of the EMBOSS package)
• eprimer3 - Pick PCR primers and hybridization oligos (part of the EMBOSS package)
• Eugene - Find eukaryotic genes using several sources of evidence
• extractfeat - Extract features from a sequence (part of the EMBOSS package)
• GENSCAN - Predict the locations and exon-intron structures of genes in genomic sequences from a variety of organisms
• getorf - Find and extract open reading frames (ORFs) (part of the EMBOSS package)
• Glimmer (Gene Locator and Interpolated Markov Modeler) - System for finding genes in microbial DNA, especially the genomes of bacteria and archaea using interpolated Markov models
• GrailEXP - Predict exons, genes, promoters, poly-As, CpG islands, EST similarities and repetitive elements within DNA sequence
• infoseq - Display simple information about sequences (part of the EMBOSS package)
• MAGPIE (Multipurpose Automated Genome Project Investigation Environment) - Identify genomic features within regions of the input sequence and construct static logical models of molecular systems from the features encoded in the genome
• Manatee - a web-based gene evaluation and genome annotation tool that can view, modify and store annotation for prokaryotic and eukaryotic genomes
• marscan - Find matrix attachment region (MAR) and scaffold attachment region (SAR) sites in nucleic acid sequences (part of the EMBOSS package)
• maskfeat - Mask off features of a sequence (part of the EMBOSS package)
• plotorf - Plot potential open reading frames (ORFs) (part of the EMBOSS package)
• primersearch - Search DNA sequences for matches with primer pairs (part of the EMBOSS package)
• Qrna - Detect conserved RNA secondary structures, including both ncRNA genes and cis-regulatory RNA structures, using comparative genome sequence analysis
• recoder - Remove restriction sites but maintain same translation (part of the EMBOSS package)
• redata - Search REBASE for enzyme name, references, suppliers and more (part of the EMBOSS package)
• remap - Display a sequence with restriction sites, translation and more (part of the EMBOSS package)
• restover - Find restriction enzymes producing a specific overhang (part of the EMBOSS package)
• restrict - Find restriction enzyme cleavage sites (part of the EMBOSS package)
• showfeat - Show features of a sequence (part of the EMBOSS package)
• showorf - Pretty output of DNA translations (part of the EMBOSS package)
• showseq - Display a sequence with features, translation and more (part of the EMBOSS package)
• silent - Scan for silent mutation restriction enzymes (part of the EMBOSS package)
• sixpack - Display a DNA sequence with six-frame translation and open reading frames (ORFs) (part of the EMBOSS package)
• stssearch - Search a DNA database for matches with a set of STS primers (part of the EMBOSS package)
• tcode - Fickett TESTCODE statistic to identify protein-coding DNA (part of the EMBOSS package)
• tfscan - Scan DNA sequences for transcription factors (part of the EMBOSS package)
• tRNAscan - Search for tRNA genes in a genomic sequence
• twofeat - Find neighboring pairs of features in sequences (part of the EMBOSS package)
• wobble - Wobble base plot (part of the EMBOSS package)