scopseqs adds PDB and SWISS-PROT sequence records to a scop classification file.

This is part of Jon Ison's protein structure analysis package. This package is still being developed. Please ignore this program until further details can be documented. All further queries should go to Jon Ison ([email protected]).

Here is a sample session with scopseqs:

% scopseqs

Mandatory qualifiers:

[-scopin] (infile)

Name of scop file for input (EMBL-like format).

[-pdbtosp] (infile)

Name of the pdbcodes to SWISS-PROT indexing (EMBL-like format).

[-dpdb] (string)

Location of clean domain coordinate files for input (EMBL-like format).

[-extn] (string)

File extension of clean domain coordinate files.

[-scopout] (outfile)

Name of processed file for output (EMBL-like format).

[-errf] (outfile)

Name of log file for the build.

Advanced qualifiers:

-datafile (matrixf)

This is the scoring matrix file used when comparing sequences.

-gapopen (float)

The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.

-gapextend (float)

The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps. You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.