| Online Tool | Description |
|---|
| > Also see Primer Design Tools | |
| AmiGene | Annotation of Microbial Genes for for automatically identifying the most likely CoDing Sequences (CDSs). |
| BCM: Multiple Sequence Alignments | Alignment of multiple DNA or protein sequences. |
| BCM: Pairwise Sequence Alignment | Optimal sequence alignment of two sequences in Fasta format. |
| BCM: Sequence Utilities | Conversion of sequences to FASTA format. Primer selection. Restriction maps. Translations. Reverse complement and reverse nucleotide sequences. |
| Biology WorkBench | Protein tools: structure prediction, blast, multiple sequence alignment, randomize sequence. Nucleic tools: Primer design. |
| 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. |
| ConSeq Server | Server for the identification of functionally and structurally important residues in protein sequences. |
| Count codon | Codon usage analysis. |
| Countcodon | Generates a codon usage table for the input sequence. |
| CpGplot | Program to plot CpG rich areas in a nucleic acid sequence |
| FMAP | Sequence alignment with genome. Maps sequence to human, rat and mouse genomes. |
| 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. |
| make-na | Automatic production of DNA double helix with sequence input. |
| Molecular Toolkit | Programs for analysis and manipulation of nucleic acid and protein sequence. Includes dot plot similarity matrix, inverse, complement, double-stranded conversions. |
| 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). |
| 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 Mapper | Maps sites for restriction enzymes (restriction endonucleases) in DNA sequences. |
| REviewer | Web server generates restriction enzyme maps of linear or circular sequences. Output can be in SVG (Scalable Vector Graphics) format. |
| RNA/DNA secondary structure prediction and design | PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules. |
| Sequence Manipulation Suite | JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. |
| siRNA Target Finder | siRNA design guidelines. SiRNA is used for gene silencing. |
| SOAP Short Oligonucleotide Analysis | Program for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis. |
| Superlink | Genetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs. |
| TFSEARCH | Reports transcription factor binding sites on input DNA sequence. |
| Trait-o-matic | Open-source tool to find and classify phenotypic correlations for variations in whole genomes. |
| WebACT | Online visualisation of comparisons between up to five prokaryotic genome sequences, using Artemis Comparison Tool (ACT). |
| WEGO | Web Gene Ontology Annotation Plot. |
