seqretsplit

seqretsplit

seqretsplit reads and writes (returns) sequences in individual files. seqretsplit is exactly the same as seqret , except it writes each sequence to an individual file that when writing out more than one sequence. Therefore, its main use is to split a file containing multiple sequences into many files, each containing one sequence.

Here is a sample session with seqretsplit :

% seqretsplit
Reads and writes (returns) sequences in individual files
Input sequence(s): embl:hsfa11*
Output sequence [hsfa110.fasta]:

The specification of the output file is not used in this case. At some point this ought to change, and you will not be prompted for the output file.

Mandatory qualifiers:

[-sequence] (seqall): Sequence database USA.
[-outseq] (seqoutall): Output sequence(s) USA.

Advanced qualifiers:

-firstonly (boolean): Read one sequence and stop.

seqsearch

seqsearch generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments.

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 (jison@hgmp.mrc.ac.uk).

Here is a sample session with seqsearch :

% seqsearch

Mandatory qualifiers:

[-escop] (infile): Name of scop classification file (EMBL format input).
[-align] (string): Location of scop alignment files (input).
[-alignextn] (string): Extension of scop alignment files.
-niter (integer): Number of PSI-BLAST iterations.
-evalue (float): Threshold E-value for inclusion in family.
-maxhits (integer): Maximum number of hits.
-submatrix (string): Residue substitution matrix.
[-hits] (string): Location of scop hits files (output).
[-hitsextn] (string): Extension of scop hits files.
-logf (outfile): Name of log file for the build.

seqsort

seqsort reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file.

Here is a sample session with seqsort :

% seqsort

Mandatory qualifiers ( bold if not always prompted):

-mode (menu): Select mode.
- psipath ( string): Location of scop hits files (input).
- psiextn ( string): Extension of scop hits files.
- swisspath ( string): Location of seqwords hits files.
- swissextn ( string): Extension of seqwords input files.
- psifile ( string): Name of file containing processed scop hits file (input).
- swissfile ( string): Name of file containing processed seqwords hits file (input).
-overlap (integer): number of overlapping residues required for merging of two hits.
[-hitsf] (outfile): Name of scop hits file (output).
[-validf] (outfile): Name of validation file (output).