| Online Tool | Description |
|---|---|
| @ 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. |
| ConSeq Server | Server for the identification of functionally and structurally important residues in protein sequences. |
| Countcodon | Generates a codon usage table for the input sequence. |
| Cpgreport | Identify and report CpG islands in nucleotide sequences. |
| EMBOSS Seqret | Sequence format conversion. Reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions. |
| 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. |
| 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. |
| PromoSer | Web-based service for extraction of a large number of promoter sequences from mammalian genomes. |
| RNA/DNA secondary structure prediction and design | PairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules. |
| 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. |
| 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). |
| TRACTS | A program to map oligopurine.oligopyrimidine and other binary DNA tracts. |
| 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. |
- Download software patches ›. Sequencing Analysis Software uses a base-caller algorithm that performs base calling for pure and mixed base calls. The software analyzes, displays, edits, saves, and prints sample files that are generated from Applied Biosystems DNA analyzers and genetic analyzers.
- A great all-round tool. Cn3D say it out loud “see in 3D”. This great piece of software from NCBI is a sequence viewer with a difference. Not only does it perform 2D alignments, but it also allows the user to see the position residues in the 3D protein sequence. Great for mutagenesis studies.
Sanger Sequencing Analysis Tools
Sequence Analysis Software Free Mac Online
CodonCode Aligner - A powerful sequence alignment program for Windows and Mac OS X. Free demo downloads (no forms), 30-day fully functional trial. MEGA - A free tool for sequence alignment and phylogenetic tree building and analysis. Integrated web interface for BLAST searches and GenBank browsing. Free Sequence Alignment Software.