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SEQSORT documentation |
CL Alpha and beta proteins (a+b) XX FO Ferredoxin-like XX SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain XX SI 54894 XX NS 27 XX NN [1] XX TY HIT XX SC 0.00 XX AC Q9YBD5 XX RA 11 START; 105 END; XX SQ SEQUENCE 95 AA; 10687 MW; B8ACF34B CRC32; VRKIRSGVVI DHIPPGRAFT MLKALGLLPP RGYRWRIAVV INAESSKLGR KDILKIEGYK PRQRDLEVLG IIAPGATFNV IEDYKVVEKV KLKLP XX NN [2] XX TY HIT XX SC 0.00 XX AC Q9UX07 XX RA 12 START; 104 END; XX SQ SEQUENCE 93 AA; 10312 MW; 12DDDE7C CRC32; VSKIRNGTVI DHIPAGRALA VLRILGIRGS EGYRVALVMN VESKKIGRKD IVKIEDRVID EKEASLITLI APSATINIIR DYVVTEKRHL EVP XX NN [3] XX TY HIT XX SC 0.00 XX AC Q9KP65 XX RA 9 START; 100 END; XX [Part of this file has been deleted for brevity] MMFHKIYIQK HDNVSILFAD IEGFTSLASQ CTAQELVMTL NELFARFDKL AAENHCLRIK ILGDCYYCVS GLPEARADHA HCCVEMGVDM IEAISLVREV TGVNVNMRVG IHSGRVHCGV LGLRKWQFDV WSNDVTLANH MEAGGRAGRI HITRATLQYL NGDYEVEPGR GGERNAYLKE QHIETFLIL XX NN [111] XX TY HIT XX SC 0.00 XX AC O30820 XX RA 241 START; 400 END; XX SQ SEQUENCE 160 AA; 17506 MW; B1E1A024 CRC32; NIIADKYDEA SVLFADIVGF TERASSTAPA DLVRFLDRLY SAFDELVDQH GLEKIKVSGD SYMVVSGVPR PRPDHTQALA DFALDMTNVA AQLKDPRGNP VPLRVGLATG PVVAGVVGSR RFFYDVWGDA VNVASRMEST DSVGQIQVPD EVYERLKDDF XX NN [112] XX TY HIT XX SC 0.00 XX AC O19179 XX RA 877 START; 1032 END; XX SQ SEQUENCE 156 AA; 17212 MW; 675838EA CRC32; PEYFEEVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM VASGLPQRNG QRHAAEIANM ALDILSAVGS FRMRHMPEVP VRIRIGLHSG PCVAGVVGLT MPRYCLFGDT VNTASRMEST GLPYRIHVNM STVRIL XX NN [113] XX TY HIT XX SC 0.00 XX AC O02740 XX RA 877 START; 1042 END; XX SQ SEQUENCE 166 AA; 18151 MW; E2BB2824 CRC32; PEGFDLVTLY FSDIVGFTTI SAMSEPIEVV DLLNDLYTLF DAIIGSHDVY KVETIGDAYM VASGLPKRNG MRHAAEIANM SLDILSSVGT FKMRHMPEVP VRIRIGLHSG PVVAGVVGLT MPRYCLFGDT VNTASRMEST GLPYRIHVSH STVTILRTLG EGYEVE XX // |
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Standard (Mandatory) qualifiers (* if not always prompted): [-dhfindir] directory This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. -overlap integer This option specifies the number of overlapping residues required for merging of two hits. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. -dofamilies toggle This option specifies to write a domain families file. If this option is set a domain families file is written. -doambiguities toggle This option specifies whether to write a domain ambiguities file. If this option is set a domain ambiguities file is written. [-dhfoutdir] outdir This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. * -hitsfile outfile This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). * -ambigfile outfile This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-hitsfile" associated qualifiers -odirectory string Output directory "-ambigfile" associated qualifiers -odirectory 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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[-dhfindir] (Parameter 1) |
This option specifies the location of DHF files (domain hits files) (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Directory | ./ |
-overlap | This option specifies the number of overlapping residues required for merging of two hits. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits. | Any integer value | 10 |
-dofamilies | This option specifies to write a domain families file. If this option is set a domain families file is written. | Toggle value Yes/No | No |
-doambiguities | This option specifies whether to write a domain ambiguities file. If this option is set a domain ambiguities file is written. | Toggle value Yes/No | No |
[-dhfoutdir] (Parameter 2) |
This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL-like). The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. | Output directory | ./ |
-hitsfile | This option specifies the name of domain families file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | fam.dhf |
-ambigfile | This option specifies the name of domain ambiguities file (output). A 'domain families file' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e.g. by using SEQSEARCH (psiblast). The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | Output file | oth.dhf |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
% seqsort Reads multiple files of hits and writes (i) a scop families file and (ii) a scop ambiguities file. Mode of operation 1 : Process psiblast hits 2 : Process swissparse hits (WARNING - untested) 3 : Merge psiblast and swissparse hits (WARNING - untested) Select mode [1]: Location of scop hits files (input) [./]: structure Extension of scop hits files (input) [.hits]: Number of overlapping residues required for merging of two hits [10]: 20 Name of scop families file (output) [fam.hits]: scop.fam Name of ambiguities file (output) [oth.hits]: scop.oth Warning: Empty list in embDmxScophitsToHitlist Warning: Empty list in embDmxScophitsToHitlist Warning: Empty list in embDmxScophitsToHitlist |
Go to the output files for this example
All DHF files (of the file extension .dhf specicied in ACD) in
directory /test_data were processed by SEQSORT. DHF output files were
written to /test_data/seqsort/seqsort_hits. A shared segment of 10 or
more identical was required to class two sequences as overlapping.
Domain families and ambiguities files called fam.dhf and oth.dhf
respectively were written to /test_data/seqsort.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Domain hits file | DHF format (FASTA-like with domain classification information). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST) | N.A. |
Domain families & ambiguities file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from PSIBLAST searches of a sequence database. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a 'domain ambiguities file'. | The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file). | N.A. | |
Domain validation file | Contains sequence relatives (hits) for each of a number of different SCOP or CATH families, superfamilies and folds. The file contains the collated results from PSIBLAST searches of a sequence database for the indvidual families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a superfamily or fold instead. | The domain validation file is generated by using SEQNR and uses the same format as a DHF file (domain hits file). | N.A. |
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 |
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 |
sigscan | Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database |
See also http://emboss.sourceforge.net/