| @ Primer Design Tools | |
| 3DNA | Software system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures |
| AmiGene | Annotation of Microbial Genes for for automatically identifying the most likely CoDing Sequences (CDSs). |
| BLAST Search of Nucleotide, Protein and Genome Databases | Compare your query sequence to the working draft sequence of the human genome or its mRNA and protein products. |
| Biology WorkBench | Protein tools: structure prediction, blast, multiple sequence alignment, randomize sequence. Nucleic tools: Primer design. |
| CD-HIT | A series of programs for sequence comparisons. Creating non-redundant datasets for proteins. Clustering analysis of various types of DNAs and RNAs. Clustering 16S rRNA tags into OTUs (454, Iontorrent and Illumina reads). Generate protein families. Merge assembled contigs. |
| Countcodon | Generates a codon usage table for the input sequence. |
| Cpgreport | Identify and report CpG islands in nucleotide sequences. |
| EMBOSS Seqret | EMBOSS Seqret reads and reformats biosequences. |
| GeneMark | Gene Prediction in Bacteria, Archaea and Metagenomes. |
| Genscan | Predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms. |
| MEME Suite | Motif-based analysis of DNA, RNA and protein sequences. |
| NEBcutter | Examines DNA sequence to find large, non-overlapping open reading frames (ORFs) and sites for all restriction enzymes that cut the sequence just once. |
| ORF Finder | ORF Finder (Open Reading Frame Finder). |
| PROMALS3D | Alignments for multiple protein sequences or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures. |
| Pictogram | Tool to visualize sequence alignments and consensus sequences showing the relative frequencies of the bases at each position. |
| PlasMapper | Generates and annotates plasmid maps using only plasmid DNA sequence as input. Figures may be rendered in PNG, JPG, SVG or SVGZ format. |
| Restriction Map Generator | Analyzes a DNA sequence to identify Restriction Enzyme Sites and generate a comprehensive map overview of their locations within the DNA sequence. |
| Restriction Mapper | Maps sites for restriction enzymes (restriction endonucleases) in DNA sequences. |
| SOAP Short Oligonucleotide Analysis | Program for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis. |
| Sequence Manipulation Suite | JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. |
| Softberry | Software for next generation sequencing technologies, transcriptome analysis (with RNASeq data), SNP detection and selection of disease specific SNP subsets |
| Superlink | Genetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs. |
| TFBIND | Searching transcription factor binding sites (TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS). |
| Trait-o-matic | Open-source tool to find and classify phenotypic correlations for variations in whole genomes. |
| VIROME | Classification of predicted open-reading frames (ORFs) from viral metagenomes. |
| Vista | Programs and databases for comparative analysis of genomic sequences. |
| WEGO | Web Gene Ontology Annotation Plot. |
