Using the AnDom-Sever
Description
This WEB tool helps to assign structual domains to protein sequences and to
classify them according to
SCOP.
Input Format
Accepted are accession-no or protein-identifier like:
KPY1_ECOLI or P14178 or 2506795
You can paste your 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.
NEW (010803)
Choose between the program IMPALA or RPS-BLAST (Reverse PSI-BLAST)
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.
Note! 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) mask off segments of the query
sequence that have low compositional complexity.
Steffen Schmidt
Last modified: Wed May 26 10:12:04 EDT 2004