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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 posts 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 retrievalhttp://www.bioinformatics.nl/tools/seqatoms/cgi-bin/getseqs? Parametersdb=(pdb_seqatms|pdb_seqres|disprot|cath)id=your_id Examples
To extract PDB chain 102L_A from SEQATOMs, use: |
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 BLASThttp://www.bioinformatics.nl/tools/seqatoms/cgi-bin/blastsearch? Parameters
db=(pdb_seqatms|pdb_seqres|disprot|cath) Examples
A short sequence can be submitted via the URL: |
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 searchinghttp://www.bioinformatics.nl/tools/seqatoms/cgi-bin/keysearch? Parameters
db=(pdb_seqatms|pdb_seqres|disprot|cath) ExamplesNote: replace spaces in the words string with '%20' or '+' as shown below.
keysearch?db=pdb_seqatms&words=blood+apple&extract=1 |
Version 1.0 SEQATOMs; Last Modified 11 Dec, 2017 by BB |