Interpreting PatScan Results

PatScan offers search results in two forms:
  1. The results of the search are emailed to the address you provide.
  2. The results are stored as an HTML file which you can access and download. The URL of this file is emailed to the address you provide. The ID numbers are links which you can follow to view the EMBL, Swiss-Prot or PDB database information about the matched sequence.

Protein Search Results

PatScan offers searches the of the Swiss-Prot, TrEMBL (Translated EMBL), and the PDB protein sequence databases.

Results should look something like: 

	all
	any(TS) 1...1 GP 1...1 G 4...4 any(LFIVM) G
	sp|P02461|CA13_HUMAN:[1120,1131]:  S P GP A G QQGA I G
	sp|P02461|CA13_HUMAN:[1132,1143]:  S P GP A G PRGP V G
	.
	.
	.
	sp|P42382|CH60_EHRCH:[29,40]    :  T A GP K G LTVA I G
	sp|Q01149|CA21_MOUSE:[749,760]  :  T K GP K G ENGI V G
	COMPLETED REQUEST

The first line indicates that PatScan searched the entire database, and the second line returns the pattern you input. Subsequent lines list the matches to this pattern found in the database. For example: 

	sp|P02461|CA13_HUMAN:[1120,1131]:  S P GP A G QQGA I G
can be broken up into 5 fields. 
	sp  |  P02461  |  CA13_HUMAN  :  [1120,1131]  :  S P GP A G QQGA I G
        |         |           |               |                   |
        |         |           |               |                   |
   Swiss-Prot     |     Swiss-Prot ID    position of       matched sequence
    database      |                    matched sequence 
    searched      |
              Swiss-Prot
	    Accession number
The output is in alphabetical order based on the first character of the first pattern unit (in this case S first, then T). The matched sequence is broken into 8 segments to match the 8 pattern units of the input pattern. In the above example this breaks up as: 
	any(TS) 1...1 GP 1...1 G 4...4 any(LFIVM) G
             |    |   |    |   |   |         |    |
             S    P   GP   A   G  QQGA       I    G
TrEMBL sequences have been assigned SwissProt accession numbers, and the sequences can be accessed at the Swiss_Prot web site.
For example, you can access the Swiss-Prot database to get complete information about the protein sequence in which the matched sequence occurs, using: You may want to bookmark these links if you use them often.

The results for PDB sequence searches are essentially the same. 

	pepi 4...4 grng
	pdb|0ric_B:[7,18] : PEPI VRIV GRNG
	pdb|2aai_B:[7,18] : PEPI VRIV GRNG
	COMPLETED REQUEST
These can be broken up as follows: 
	pdb|0ric_B:[7,18] : PEPI VRIV GRNG
        |     |      |             |
        |     |      |             |
       PDB    |    position of     |
    database  |  matched sequence  | 
    searched  |                    |
	      |                    |
         PDB ID Code         matched sequence
       including chain`
The PDB ID code for this example is 0ric and the chain is the B chain.

Nucleotide Search results

PatScan searches the EMBL Nucleotide Sequence Database maintained by EBI.

Results should look something like: 

	fungi
	p1=2...2 3...4  p2=4...5  3...3 ~p2 2...3 ~p1
	embl|A02534:[1009,1028]  :  aa acc  cagc  agg gctg  gg  tt
	embl|A06260:[1501,1521]  :  aa ata  taag  gaa ctta  tga tt
	.
	.
	.
	embl|Z50840:[2998,3019]  :  tt agct ctct  aga agag  tgt aa
	embl|Z67741:[458,478]    :  tt gcg  gcgc  ctt gcgc  cag aa
	COMPLETED REQUEST
The first line indicates that PatScan searched the fungi database, and the second line returns the pattern you input. Subsequent lines list the matches to this pattern found in the database. For example: 
        embl|A02534:[1009,1028]  :  aa acc  cagc  agg gctg  gg  tt
can be broken up into 4 fields. 
	embl  |  A02534  :  [1009,1028]      :  aa acc  cagc  agg gctg  gg  tt
         |          |            |                         |
	 |          |            |                         |
        EMBL       EMBL      position of           matched sequence 
      database   Accession   matched sequence
      searched    Number
The output is in alphabetical order based on the first character of the first pattern unit (in this case AA first, with TT last). The matched sequence is broken into 8 segments to match the 8 pattern units of the input pattern. In the above example this breaks up as: 
        p1=2...2 3...4  p2=4...5  3...3 ~p2 2...3 ~p1
             |     |         |      |    |    |    |
	     aa   acc       cagc   agg  gctg  gg   tt
You can access the EMBL database to get complete information about the nucleotide sequence in which the matched sequence occurs, using: You may want to bookmark this link if you use it often.