Sequences submitted to the Sequence Manipulation Suite 2 do not leave your computer and are instead manipulated by your web browser, which executes the JavaScript. The Sequence Manipulation Suite 2 was written by Paul Stothard (University of Alberta, Canada). Send questions and comments to stothard@ualberta.ca.
Here are short descriptions of the programs that comprise the Sequence Manipulation Suite 2:
- Combine FASTA - converts multiple FASTA sequence records into a single sequence. Use Combine FASTA, for example, when you wish to determine the codon usage for a collection of sequences using a program that accepts a single sequence as input.
- EMBL to FASTA - accepts an EMBL file as input and returns the entire DNA sequence in FASTA format. Use this program when you wish to quickly remove all of the non-DNA sequence information from an EMBL file.
- EMBL Feature Extractor - accepts an EMBL file as input and reads the sequence feature information described in the feature table. The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. EMBL Feature Extractor is particularly helpful when you wish to derive the sequence of a cDNA from a genomic sequence that contains many introns.
- EMBL Trans Extractor - accepts an EMBL file as input and returns each of the protein translations described in the file in FASTA format. EMBL Trans Extractor can be used when you are more interested in the predicted protein translations of a DNA sequence than the DNA sequence itself.
- Filter DNA - removes non-DNA characters from text. Use this program when you wish to remove digits and blank spaces from a sequence to make it suitable for other applications.
- Filter Protein - removes non-protein characters from text. Use this program when you wish to remove digits and blank spaces from a sequence to make it suitable for other applications.
- GenBank to FASTA - accepts a GenBank file as input and returns the entire DNA sequence in FASTA format. Use this program when you wish to quickly remove all of the non-DNA sequence information from a GenBank file.
- GenBank Feature Extractor - accepts a GenBank file as input and reads the sequence feature information described in the feature table, according to the rules outlined in the GenBank release notes. The program extracts or highlights the relevant sequence segments and returns each sequence feature in FASTA format. GenBank Feature Extractor is particularly helpful when you wish to derive the sequence of a cDNA from a genomic sequence that contains many introns.
- GenBank Trans Extractor - accepts a GenBank file as input and returns each of the protein translations described in the file in FASTA format. GenBank Trans Extractor should be used when you are more interested in the predicted protein translations of a DNA sequence than the DNA sequence itself.
- One to Three - converts single letter translations to three letter translations.
- Range Extractor - accepts a DNA sequence along with a set of positions or ranges. The bases corresponding to the positions or ranges are returned, either as a single new sequence, a set of FASTA records, or as uppercase text inside of the original lowercase sequence. Use Range Extractor to obtain subsequences using position information.
- Reverse Complement - converts a DNA sequence into its reverse, complement, or reverse-complement counterpart. The entire IUPAC DNA alphabet is supported, and the case of each input sequence character is maintained. You may want to work with the reverse-complement of a sequence if it contains an ORF on the reverse strand.
- Three to One - converts three letter translations to single letter translations. Digits and blank spaces are removed automatically. Non-standard triplets are ignored.
- Group DNA - adjusts the spacing of DNA sequences and adds numbering. You can specify the group size (the number of bases per group), as well as the number of bases per line. The output of this program can serve as a convenient reference, since the numbering and spacing allows you to quickly locate specific bases.
- Group Protein - adjusts the spacing of protein sequences and adds numbering. You can specify the group size (the number of residues per group), as well as the number of residues per line. The output of this program can serve as a convenient reference, since the numbering and spacing allows you to quickly locate specific residues.
- Multiple Align Conservation - accepts a group of aligned sequences (in FASTA or GDE format) and colors the alignment. The program examines each residue and compares it to the other residues in the same column. Residues that are identical among the sequences are given a black background, and those that are similar among the sequences are given a gray background. The remaining residues receive a white background. You can specify the percentage of residues that must be identical and similar for the coloring to be applied. Use Multiple Align Conservation to enhance the output of sequence alignment programs.
- Multiple Align Properties - accepts a group of aligned sequences (in FASTA or GDE format) and colors the alignment. The program examines each residue and compares it to the other residues in the same column. Residues that are identical or similar among the sequences are given a colored background. The color is chosen according to the biochemical properties of the residue. You can specify the percentage of residues that must be identical and similar for the coloring to be applied. Use Multiple Align Properties to highlight protein regions with conserved biochemical properties.
- Primer Map - accepts a DNA sequence and returns a textual map showing the annealing positions of PCR primers. Restriction endonuclease cut sites, and the protein translations of the DNA sequence can also be shown. Use this program to produce a useful reference figure, particularly when you have designed a large number of primers for a particular template. Primer Map uses the standard genetic code and supports the entire IUPAC alphabet.
- Restriction Map - accepts a DNA sequence and returns a textual map showing the positions of restriction endonuclease cut sites. The translation of the DNA sequence is also given, in the reading frame you specify. Use the output of this program as a reference when planning cloning strategies. Restriction Map uses the standard genetic code and supports the entire IUPAC alphabet.
- Translation Map - accepts a DNA sequence and returns a textual map displaying protein translations. The reading frame of the translation can be specified (1, 2, 3, or all three), or you can choose to treat uppercase text as the reading frame. Translation Map uses the standard genetic code and supports the entire IUPAC alphabet.
- Random DNA Sequence - generates a random sequence of the length you specify. Random sequences can be used to evaluate the significance of sequence analysis results.
- Random Protein Sequence - generates a random sequence of the length you specify. Random sequences can be used to evaluate the significance of sequence analysis results.
- Sample DNA - randomly selects bases from the guide sequence until a sequence of the length you specify is constructed. Each selected base is replaced so that it can be selected again.
- Sample Protein - randomly selects bases from the guide sequence until a sequence of the length you specify is constructed. Each selected residue is replaced so that it can be selected again.
- Shuffle DNA - randomly shuffles a DNA sequence. Shuffled sequences can be used to evaluate the significance of sequence analysis results, particularly when sequence composition is an important consideration.
- Shuffle Protein - randomly shuffles a protein sequence. Shuffled sequences can be used to evaluate the significance of sequence analysis results, particularly when sequence composition is an important consideration.
