SEQATOMs

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SEQATOMs services

You can access the protein sequences in SEQATOMs easily via the URL (URL-API). BLAST searches can also be executed via the URL (you can submit multiple sequences). An example Perl script that post sequences to the SEQATOMs BLAST service is also provided below.

Please cite: Brandt, B.W., Heringa, J. and Leunissen, J.A.M. (2008). SEQATOMS: a web tool for identifying missing regions in PDB in sequence context. Nucleic Acids Reseach 36:W255-W259.

Access to the FASTA sequences

You can access sequences in SEQATOMs via a URL. The ID has to be exactly as in the source databases, with one exception: PDB SEQATOMS accepts IDs in any letter casing.

Reference for ID retrieval

http://www.bioinformatics.nl/tools/seqatoms/cgi-bin/getseqs?

Parameters

Examples

To extract PDB chain 102L_A from SEQATOMs, use:
getseqs?db=pdb_seqatms&id=102L_A
getseqs?db=cath&id=1gmeA00
getseqs?db=disprot&id=DP00445

To extract multiple sequences at once, you can repeat the id=your_id or seperate the identifiers by commas. For example:
Note: these links return HTML; calling this URL directly returns plain text records.
getseqs?db=cath&id=1gmeA00&id=2afgC00
getseqs?db=disprot&id=DP00445&id=DP00001
getseqs?db=disprot&id=DP00445,DP00001

Remote BLAST

Remote BLASTing is supported for XML output only. The XML returned is the standard NCBI XML output, however, hit and homology strings have been replaced with to show the lower-case letters.

Reference for BLAST

http://www.bioinformatics.nl/tools/seqatoms/cgi-bin/blastsearch?

Parameters

db=(pdb_seqatms|pdb_seqres|disprot|cath)
seq=your seq as string
fname=file name of your sequence file
mask=(0|1) masking character 0: lower-case (default); 1: "x"
expect=10 E-value threshold; default: 10
descript=100 Number of descriptions; default: 100;
align=100 Number of alignments; default: 100;

Examples

A short sequence can be submitted via the URL:
blastsearch?db=pdb_seqatms&seq=MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMR

However, we prefer you POST your queries to the server. You could use this Perl script to automatically POST your sequences. Possibly, you need to install the Perl's LWP for this to work (likely if you are using Mac OS X).

Identifier searches

Remote keyword searches are best executed per database. The PDB SEQATOMs (pdb_seqatms) FASTA records contain the most extensive sequence description. See the examples in the database descriptions. Wildcard searching is not available in case of automated access.

Reference for identifier searching

http://www.bioinformatics.nl/tools/seqatoms/cgi-bin/keysearch?

Parameters

db=(pdb_seqatms|pdb_seqres|disprot|cath)
words=your keywords as string
and=(1|0) Search for all (default) keywords or any
extract=(0|1) extract FASTA sequences; default: 0

Examples

keysearch?db=pdb_seqatms&words=blood+apple&extract=1
keysearch?db=pdb_seqatms&words=blood%20apple&extract=1
keysearch?db=cath&words=acidic