Nucleic Acids Research Advance Access originally published online on May 7, 2008
Nucleic Acids Research 2008 36(Web Server issue):W255-W259; doi:10.1093/nar/gkn237
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W255-W259
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
1Centre for Integrative Bioinformatics (IBIVU), VU University Amsterdam, De Boelelaan 1081a, 1081 HV Amsterdam and 2Laboratory of Bioinformatics, Wageningen University, PO Box 8128, 6700 ET Wageningen, the Netherlands
*To whom correspondence should be addressed. Tel: +31 20 59 87816; Fax: +31 20 59 87653; Email: bwbrandt{at}few.vu.nl
Received January 31, 2008. Revised March 31, 2008. Accepted April 15, 2008.
With over 46 000 proteins, the Protein Data Bank (PDB) is the most important database with structural information of biological macromolecules. PDB files contain sequence and coordinate information. Residues present in the sequence can be absent from the coordinate section, which means their position in space is unknown. Similarity searches are routinely carried out against sequences taken from PDB SEQRES. However, there no distinction is made between residues that have a known or unknown position in the 3D protein structure. We present a FASTA sequence database that is produced by combining the sequence and coordinate information. All residues absent from the PDB coordinate section are masked with lower-case letters, thereby providing a view of these residues in the context of the entire protein sequence, which facilitates inspecting ‘missing’ regions. We also provide a masked version of the CATH domain database. A user-friendly BLAST interface is available for similarity searching. In contrast to standard (stand-alone) BLAST output, which only contains upper-case letters, our output retains the lower-case letters of the masked regions. Thus, our server can be used to perform BLAST searching case-sensitively. Here, we have applied it to the study of missing regions in their sequence context. SEQATOMS is available at http://www.bioinformatics.nl/tools/seqatoms/.
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