Using the AnDom-Server
DescriptionThis web-based tool helps to assign structural domains to protein sequences and to classify them according to SCOP.
Protein-IdentifiersAccepted are accession-numbers or protein-identifiers like:
KPYK1_ECOLI or P0AD61 or AAB47952
Protein-SequenceYou can paste your protein sequence either in FASTA-format or simply the bare sequence. A sequence in FASTA-format starts with the character '>' followed by a single-line description of the sequence. The following lines then contain the sequence.
MethodChoose between the programs IMPALA, RPS-BLAST (Reverse PSI-BLAST) and RPS-BLAST-PLUS (BLAST+ package).
Excerpt from README.rps provided with the BLAST package:
RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles. This is the opposite of PSI-BLAST that searches a profile against a database of sequences, hence the 'Reverse'. RPS-BLAST uses a BLAST-like algorithm, finding single- or double-word hits and then performing an ungapped extension on these candidate matches. If a sufficiently high-scoring ungapped alignment is produced, a gapped extension is performed and those (gapped) alignments with sufficiently low expect value are reported. This procedure is in contrast to IMPALA that performs a Smith-Waterman calculation between the query and each profile, rather than using a word-hit approach to identify matches that should be extended.
DatabaseHere you can choose between different versions of SCOP. For each version PSSMs were newly calculated.
Note! The classification of structual domains in SCOP may change between different versions.
ExpectHere you can set the statistical significance threshold for reporting hits against the database.
FilterThe SEG filter (Wootton & Federhen, 1993) masks off segments of the query sequence that have low compositional complexity.
ShowDisplays the index list of related queries.