SiteMatcher 2.0

What's news?

The release 2.0 offers new features for registred users. The registration is free and it is just intended to filter the access and avoid the use of the web server resources by internet scanners and other not research-oriented use. Options for the registered users include multiple db scan, multiple query sequences, batch-mode with e-mail notification of work finished (very useful for massive searches).

If you are interested to register for the use, please send an e-mail to: angelo.facchiano AT . You will be contacted by e-mail as soon as possible. Note that registration of new users can be temporarely closed in the case of massive CPU usage.

NOTE: the registration is currently not possible, due to the redesigning of the services. You can send an e-mail to be informed about any news.

SITEMATCHER is a tool created to compare the amino acid sequence of a given protein to a list of short segments of some interest.

The pre-defined databases available for the searches are the ASC section: AIRS, BAC, CHAMSE, DVP, DORRS, SSP, and TRANSIT (click on the name to read more information about it).

Results will indicate what segments of your query sequence are similar to segments in the database, and the related alignments and percent of identity. Hyperlinks will give you the information about the database entries.

Short description of your query or job session (optional):

Insert here your query sequence(s) according to the FASTA format (see the Note at the end of the page for a description of the format):

Other Options

Select the database:

Show results with at least % of identity (max=100, min=40)
Some ASC sections report the annotation for the reactive amino acid(s). Check the following box to see in the output only results which match this amino acid:
Minimum extension of similarity window (3 or more):

For registred users only:

User name: E-mail address: Options:

Note: Description of the FASTA format

The FASTA format is one of the most used in bioinformatics tools to represent amino acid sequences.
The sequence in FASTA format begins with a single-line description which starts with the ">" symbol.
The second and following lines contain amino acid sequence data in the one-letter code, with a maximum of 80 characters for each line.
The following is an example of FAST format sequence:

>sw|O14810|CLX1_HUMAN Complexin 1 (Synaphin 2). 

In this interface, to facilitate Copy&Paste input, any blank space or number within the sequence lines is allowed, it will be erased before the processing of the sequence.

For any question, please contact me at the address angelo.facchiano AT