A Protein Sequence Culling Server

Pisces has several capabilities in producing subsets of sequences from larger sets:

• subsets of sequences culled from the entire PDB according to structure quality and maximum mutual sequence identity
• subsets of sequences culled from a list of PDB chains or PDB entries input by the user, according to structure quality and maximum mutual sequence identity
• subsets of sequences from user-input lists of GenBank accession numbers, according to maximum mutual sequence identity
• subsets of sequences from user-input BLAST or PSI-BLAST output; the hits are culled according to mutual sequence identity

Important features of this service:

• sequence identities for PDB sequences are determined by creating a hidden Markov model for every unique PDB sequence with the program HHblits (Söding et al.) and searching the resulting collection of HMMs with each individual HMM with the program HHsearch
• PISCES can also therefore provide meaningful results at low sequence identity (15-30%)
• non-PDB sequences are culled with sequence identities from PSI-BLAST. We do not search the non-redundant sequence database, but rather use the user's input sequences as the database. This server will usually be used to cull a related set of sequences, for instance those from a PSI-BLAST search
• the server provides output lists of accession IDs and files of the sequences in FASTA format on a webpage created for the user. The address is e-mailed to the user upon completion of the calculation, and will be stored for one week
• PDB sequences are updated weekly from the PDB mmCIF files
• PISCES now correctly handles multi-character chain IDs, which are now used in very large structures by the PDB

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