Protein Sequence Analysis

PSA finds those proteins which contain a given amino acid sequence. [ Hide ]

Drag some building blocks to Your sequence to build a query. A place can contain multiple amino acids. You can use wildcards (? *).

Scroll down for more help and terms of use.

Simple version

• The colorful building blocks correspond to amino acids and wildcards.
  • Color code: Small nonpolar, Negatively charged, Hydrophobic, Positively charged, Polar.
    This color code comes from the book Lesk, Introduction to Bioinformatics.
• The editing area is found under Your sequence and consists of slots.
• Each slot can accomodate either a wildcard (? or *), or one or more amino acids.
  • ? means any amino acid.
  • * means any amino acids (zero or more).
• You can
  • create a new slot by dragging a building block here:
  • add a block to an existing slot by dragging it into the slot
    • Wildcards replace everything already in the slot.
  • remove a block from the editing area by simply clicking it
  • rearrange slots by grabbing them by the blue handle and dragging them around
  • discard the current query and start a new one by clicking
• Click to start the search.
• An example query:
  

Advanced version (regular expressions)

• This section is intended mainly for programmers.
• Regular expressions (regex for short) are powerful tools for searching complicated patterns.
• PSA allows not only building a query in a graphical way, but advanced users can input a regex which will be matched against the sequence database.
  • As an example, the regex [AY]{5,} matches all proteins which have at least 5 consecutive A or Y. For example, the amino acid sequence DGYAYYAT is matched by this regex.
  • More information on regular expressions → here.

You can use this service only if you accept the following terms: We do not guarantee anything about this service: We do not state anything about the usability of this service, and we do not state that the results that we may return can be used for any purpose. We cannot guarantee that this service will be available in the future, and we cannot guarantee that your query would generate any output at all.