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ARTS Web Server:

The web server runs ARTS algorithm with the default values. It is recommended to use this option if you are not familier with the parameters of ARTS. If you wish to obtain more advanced alignments, you can download the software and play around with the parameters.
 
Pairwise Alignment:

Input:
  • Molecule 1/2 The user should either supply a PDB code of a nucleic acid structure or upload a PDB file. Each PDB code is a four character PDB ID, followed by a colon and a list of chain IDs, for instance '1nbs:B' and '1u9s'. Each molecule should include at least one stem
  • Email Address: A link to the output of ARTS will be sent to this email address.

Ouput:

After submitting a query, the html page will be updated every 10 seconds till the results will be obtained. Also, an email with a link to the results will be sent to the user. This link will list the top-ranking alignments found by ARTS.

Database Search:

Input:
  • Your Structure The user should either supply a file in PDB format of a nucleic acid structure. The structure should include at least one stem
  • Email Address: A link to the output of ARTS will be sent to this email address.

Ouput:

An email with a link to the results will be sent to the user. This link will list the top-ranking alignments found by ARTS.


Running ARTS:

Pairwise Alignment:

Command line:

arts <PDB file> <PDB file> [options]

where options are:
  -c, --config=configuration file     configuration file. If not specified, the default parameters are used.
  -o, --output=output file                output file. If not specified, the output will be printed into a file named arts.output


Input:

The names of two PDB files are expected in the command line. Additionally, it is expected that for each PDB file, there is a file describing the list of all base-pairs under the same directory. If the name of the PDB file is x.pdb, then the name of the base-pair file should be x.pairs. The format describing a base-pair is '<chain>:<residue>-<chain>:<residue>'. Here is an example for a base-pair file:

# FORMAT: <chain>:<residue>-<chain>:<residue> B:1-B:47
B:2-B:46
B:3-B:45
B:4-B:44
B:5-B:43
B:6-B:42
B:8-B:41
B:9-B:40
B:11-B:39
B:12-B:38

Database Search:

Command line:

arts <PDB file> -d <DB file> [options]

where options are:
  -c, --config=configuration file     configuration file. If not specified, the default parameters are used.
  -o, --output=output file                output file. If not specified, the output will be printed into a file named arts.output

Input:

Two input files are expected in the command line: (i) a query PDB file , and (ii) a file with a list of PDB files describing the structures in the database.  Additionally,, it is assumed that for each PDB file (both query and DB), there is a file describing the list of all base-pairs under the same directory. If the name of the PDB file is x.pdb, then the name of the base-pair file should be x.pairs. The format describing a base-pair is '<chain>:<residue>-<chain>:<residue>'. Here is an example for a base-pair file:

# FORMAT: <chain>:<residue>-<chain>:<residue> B:1-B:47
B:2-B:46
B:3-B:45
B:4-B:44
B:5-B:43
B:6-B:42
B:8-B:41
B:9-B:40
B:11-B:39
B:12-B:38

More Details:

Please see the README file.