Student Sequence Analysis Tools

1. Summary

These are simple online tools for exploring and playing with various concepts related to biological sequences.

2. Write messages in DNA

The Secret Coder Tool lets you play with the idea of encoding information in DNA sequences. This uses a two-step process: first, the message is “escaped” into a format that only used 64 different characters (specifically upper and lower case letters, digits, a space, and a percent sign). Any other character is escaped by using the percent sign and a code. For example, the code for an exclamation point is '%3F'. This is similar to the way messages are encoded in website URLs. The escaped message is then changed into DNA by using a three-base combination to represent each of the 64 characters (note that there are exactly 64 different three-base combinations; this is why we use 64 characters). To decode a message that has been encided this way, just reverse the process.

3. Translate nucleic acid sequences to protein

The Transcription and Translation Tool converts between DNA and RNA sequences, and translates RNA sequences to protein, using the standard genetic code.

Note that there is no 'reverse translation' button, because this does not occur in nature. Becaus of redundancies in the genetic code (64 possible codons are used to encode 21 values, for 20 amino acids plus stops), there are usually many possible nucleic acid sequences that could represent a given peptide. This means that generating nucleic acid seqeunces from protein seqeunces generates ambiguities. If you need to do this, try the Seqeunce Pattern Finder, described below.

4. Find patterns in DNA

The Sequence Pattern Finder lets you search a target DNA sequence for a particular pattern. The pattern may be a subsequence of bases, or a regular expression representing a pattern of bases. The pattern can use ambiguous base codes, and patterns can be generated starting with a peptide sequence.

Click the 'massage sequence' button to bring up your target sequence to the Sequence Massage (described below). When you are finished transforming your seqeunce in the Sequence Massager, press 'done' to transfer it back to the Pattern Finder.

5. Manipulate sequences

Use the Sequence Massager to remove comments, line breaks, numbers, etc. from DNA sequences. This tool also changes case, reverses, complements, and makes substitutions in your nucleic acid sequence.