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sigscan |
Standard (Mandatory) qualifiers: [-siginfile] infile This option specifies the name of the signature file (input). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN program. The files are generated by using SIGGEN. [-dbsequence] seqall This option specifies the name of the database to search. -sub matrixf This option specifies the residue substitution matrix. -gapo float This option specifies the gap insertion penalty. 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 EDNAMAT matrix for nucleotide sequences. -gape float This option specifies the gap extension penalty. 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. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. -nterm menu This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database. -nhits integer This option specifies the maximum number of hits to output. [-hitsfile] outfile This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database, in this case, by using SIGSCAN. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH or various types of HMM and profile by using LIBSCAN. [-alignfile] outfile This option specifies the name of the DAF (domain alignment file) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family (or other node in the structural hierarchies). The file is in DAF format (CLUSTAL-like) and is annotated with domain family classification information. The files generated by using SIGSCAN will contain a signature-sequence alignment of domain sequences returned by scanning a signature (for a family of domains) against a sequence database. Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-dbsequence" associated qualifiers -sbegin2 integer Start of each sequence to be used -send2 integer End of each sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 string Features file name "-hitsfile" associated qualifiers -odirectory3 string Output directory "-alignfile" associated qualifiers -odirectory4 string Output directory General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |||||||
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[-siginfile] (Parameter 1) |
This option specifies the name of the signature file (input). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN program. The files are generated by using SIGGEN. | Input file | Required | ||||||
[-dbsequence] (Parameter 2) |
This option specifies the name of the database to search. | Readable sequence(s) | Required | ||||||
-sub | This option specifies the residue substitution matrix. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||||
-gapo | This option specifies the gap insertion penalty. 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 EDNAMAT matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence | ||||||
-gape | This option specifies the gap extension penalty. 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. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence | ||||||
-nterm | This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database. |
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1 | ||||||
-nhits | This option specifies the maximum number of hits to output. | Any integer value | 100 | ||||||
[-hitsfile] (Parameter 3) |
This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database, in this case, by using SIGSCAN. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH or various types of HMM and profile by using LIBSCAN. | Output file | SIGSCAN.dhf | ||||||
[-alignfile] (Parameter 4) |
This option specifies the name of the DAF (domain alignment file) (output). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family (or other node in the structural hierarchies). The file is in DAF format (CLUSTAL-like) and is annotated with domain family classification information. The files generated by using SIGSCAN will contain a signature-sequence alignment of domain sequences returned by scanning a signature (for a family of domains) against a sequence database. | Output file | SIGSCAN.aln | ||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
(none) |
Program name | Description |
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contactcount | Counts specific versus non-specific contacts in a directory of cleaned protein chain contact files |
contacts | Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data |
domainalign | Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file) |
domainrep | Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first |
domainreso | Removes low resolution domains from a DCF file (domain classification file) |
interface | Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data |
libgen | Generates various types of discriminating elements for each alignment in a directory |
psiphi | Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file |
rocon | Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score |
rocplot | Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements |
seqalign | Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits |
seqfraggle | Removes fragments from DHF files (domain hits files) or other files of sequences |
seqsearch | Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST |
seqsort | Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification |
seqwords | Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt |
siggen | Generates a sparse protein signature from an alignment and residue contact data |