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Manipulation of Nucleic Acid Sequences
Properties
DNA Molecular Weight Calculate the molecular weight of DNA; single-stranded sequences are counted with a 5'-P.
Reverse Complement Convert a DNA sequence into its reverse, complement, or reverse-complement.
Alignments
Pairwise DNA Alignment Align two DNA sequences and color the resulting global alignment.
ORFs, Codons & Translation
Translation Map Generate a textual representation of DNA translation in varied reading frames.
Translate Translate one or more provided DNA sequence in the desired reading frames.
Back Translate Back Translate generates a DNA sequence representing the most likely non-degenerate coding sequence from a protein sequence and draw the corresponding translation map.
Codon Usage Calculate the number and frequency of each codon.
ORF Finder Search for open reading frames (ORFs) in the provided DNA sequences.
Transseq Translate DNA in varied formats (GCG, FASTA, EMBL, GenBank, PIR, NBRF or Phylip).
Translate DNA Online tool with varied graphical output options.
Restriction Enzymes
Restriction Map Create a sequence map showing the positions of restriction endonuclease cut sites.
Restriction Summary Summary of number and positions of commonly used restriction endonuclease cut sites.
Restriction Digest Determine the DNA sequences resulting from a restriction digest.
PCR and Primers
Primer Map Create a sequence map showing annealing positions of PCR primers, protein translation, and common restriction sites.
PCR Products Generate the PCR product from a DNA sequence and 2 primers.
Oligonucleotide Analysis Determine standard primer properties, including melting temperature, percent GC content, and PCR suitability.
Sequence Statistics, Patterns & Motifs
DNA Pattern Search Locate DNA patterns and motifs along the two strands of a DNA sequence.
CpG Islands Detect potential CpG island regions using a 200 bp window according to the method of Gardiner-Garden and Frommer (1987).
DNA Stats DNA Stats analyzes occurrences and frequency of each nucleotide and dinulceotides in the sequence.
Random Sequences
Random DNA Generates a random DNA sequence.
Random Coding DNA Generates a random coding DNA sequence.
Shuffle DNA Randomly shuffles a DNA sequence.
Seqmake Online tool to generate random sequences.
Format Conversion
Genbank to FASTA Convert a Genbank-formatted DNA sequence in FASTA format.
EMBL to FASTA Convert an EMBL-formatted DNA sequence in FASTA format.
Genbank Feature Extractor Extract sequence features from a Genbank-formatted DNA sequence.
EMBL Feature Extractor Extract sequence features from an EMBL-formatted DNA sequence.
Filter DNA Removes non-DNA characters from text including text marks, numbers, and spaces.
Format DNA Format DNA sequence output with selected line length, segments, and base numbering.
Combine FASTA Assemble multiple FATA sequences in a single sequence.

Manipulation of Protein Sequences
Properties
Protein Molecular Weight Convert a Genbank-formatted DNA sequence in FASTA format.
Protein Isoelectric Point Calculate the theoretical isoelectric point of a protein sequence.
Protein GRAVY Calculate the GRAVY (grand average of hydropathy) value for a protein sequence.
Alignments
Pairwise Protein Alignment Align two protein sequences and color the resulting global alignment.
Protein Statistics, Patterns & Motifs
Protein Pattern Search Locate patterns and motifs along the polypeptide sequence of a protein.
Protein Stats Calculate the number of occurrences of each residue in a polypeptide sequence.
Random Sequences
Random Protein Generate random protein sequences.
Shuffle Protein Shuffle protein sequences.
RandSeq Online tool to generate a random protein sequence.
Format Conversion
GenBank Trans Extractor Extract each of the protein translations described in a Genbank file.
EMBL Trans Extractor Extract each of the protein translations described in an EMBL file.
Three to One Convert three letter translations to single letter translations.
One to Three Convert single letter translations to three letter translations.
Filter Protein Removes non-protein characters from sequence text including text marks, numbers, and spaces.
Format Protein Format protein sequence with specific group size, line length and adds numbering.

 

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