SEQATOMs

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SEQATOMs Similarity Searching: Protein BLAST

Here, you can BLAST against the masked versions of the PDB, CATH and DisProt databases. The special features are the "Alignment Options" and "Output Options" (see below). The "Masking character" is used to visualize the "missing" residues. In case of DisProt, these are the regions annotated as disorded by DisProt. You can choose the number of hits displayed in the alignment graphic to get an idea of the overlap of missing regions among the hits. Missing regions are indicated in the graph by gray boxes. More...

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.

Paste a single sequence (in FASTA format) below:

Or upload a sequence file:

Locate sequences
Notice for users
BLAST version 2.13.0+

Available databases

 
Protein databases
PDB SEQATOMs, 09 Aug 2023 (masked)
PDB SEQATOMs, 14 Dec 2015 (masked)
PDB SEQATOMs, 07 Mar 2013 (masked)
CATH v3.2.0, July 2008 (masked)
DisProt v5.6, Jan 2011 (masked)
PDB SEQRES, 01 Mar 2013

Options and parameters

 
Search parameters
Filter low-complexity regions Yes No
Expectation score
Protein scoring parameters
Scoring matrix
Gap open/extension pair    
Alignment options
View
Masking character
Masking color
Output options
Number of descriptions
Number of alignments
Number of hits in alignment graphic
Word size
Word size (protein):
shim
To homepage Wageningen UR