This web-based tool helps to assign structural domains to protein sequences and to
classify them according to SCOP
Accepted are accession-numbers or protein-identifiers like:
KPYK1_ECOLI or P0AD61 or AAB47952
You 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.
Choose 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.
Here you can choose between different versions of SCOP
. For each version PSSMs
were newly calculated.
The classification of structual domains in SCOP may
change between different versions.
Here you can set the statistical significance threshold for reporting hits
against the database.
The SEG filter (Wootton & Federhen, 1993) masks off segments of the query
sequence that have low compositional complexity.
Displays the index list of related queries.
|, Steffen Schmidt|
Last modified: Mon Feb 18 07:12:08 EDT 2013