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libscan |
This program is part of a suite of EMBOSS applications that directly or indirectly make use of the protein structure databases pdb and scop. This program is part of an experimental analysis pipeline described in an accompanying document. We provide the software in the hope that it will be useful. The applications were designed for specific research purposes and may not be useful or reliable in contexts other than the described pipeline. The development of the suite was coordinated by Jon Ison to whom enquiries and bug reports should be sent (email jison@hgmp.mrc.ac.uk).
The advantage of screening a relatively small library of discriminating elements with a sequence is that it is sufficient for the sequence to detect its true family (discriminator) in the first rank for an effective prediction. This is in contrast to searching a larger sequence database to identify homology, where biologically significant hits may achieve statistically insignificant scores and therefore be missed. A library might help the detection of such proteins because they may still score their true discriminator higher than the others in the library regardless of statistical estimates. Further improvements to predictions are gained when multiple sources of evidence, in this case the different types of discriminating element, are considered.
The libscan application allows a protein sequence or sequences to be screened against the library of discriminating elements. The results of a screen are returned to the user in a library scan file containing a list of top-scoring SCOP domains rank-ordered by p-value for each individual type of discriminator, and also for all of the discriminator types in combination (combined prediction). For the combined prediction, the p-value is derived from an empirically derived distribution of the product of the p-values of the individual methods.
libscan runs in one of two modes either (i) database search mode or (ii) library screen mode. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. Each directory must contain a discriminating element for each of one or more scop families; files for indivdual families should have the same name (possibly with different file extensions) in the different directories, e.g. the scop family with the identifier 46445 might be represented by files 46445.hmm, 46445.sig, 46445.gribs and 46445.henik in their respective directories. libscan scans each discriminating element against a sequence set that must also be provided by the user and generates a signature hits file (of scored hits to sequences in the set) for each individual discriminating element. In mode (i), the user must also provide a scop validation file so that a classification of hits can be given in the signature hits files. The user specifies a maximum number of false hits that are written to the signature hits files.
In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top-scoring families) for each sequence. In either mode, a scop classification file is required as a source of family classification data. The paths and extensions of the sequence set and scop classification files (input) different types of discriminating elements (input), and paths and extension of signature hits files or library scan file (output) are specified by the user.
Standard (Mandatory) qualifiers (* if not always prompted): -mode menu Libscan runs in one of two modes either (i) database search mode or (ii) library screen mode. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top-scoring families) for each one. -db seqset In database search mode libscan scans each discriminating element against a sequence set. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) -[no]grib boolean Use Gribskov profile -[no]henik boolean Use Henikoff profile -[no]hmm boolean Use HMM profile -[no]sig boolean Use signature * -hmmpath string Location of HMM profile files (input) * -hmmextn string Extension of HMM profile files (input) * -hmmoutpath string Location of signature hits/library scan files for hmm searches (output) * -hmmoutextn string Extension of signature hits/library scan files for hmm searches (output) * -gbvpath string Location of Gribskov profile files (input) * -gbvextn string Extension of Gribskov profile files (input) * -gbvgapo float Gap insertion penalty * -gbvgape float Gap extension penalty * -gbvoutpath string Location of signature hits/library scan files for Gribskov profile searches (output) * -gbvoutextn string Extension of signature hits/library scan files for Gribskov profile searches (output) * -hnfpath string Location of Hennikoff profile files (input) * -hnfextn string Extension of Hennikoff profile files (input) * -hnfgapo float Gap insertion penalty * -hnfgape float Gap extension penalty * -hnfoutpath string Location of signature hits/library scan files for Henikoff profile searches (output) * -hnfoutextn string Extension of signature hits/library scan files for Henikoff profile searches (output) * -sigpath string Location of signature files (input) * -sigextn string Extension of signature files (input) * -nterm menu Select number * -sub matrixf Residue substitution matrix * -siggapo float Gap insertion penalty * -siggape float Gap extension penalty * -sigoutpath string Location of signature hits/library scan files for signature searches (output) * -sigoutextn string Extension for signature hits/library scan files for signature searches (output) -scopf infile In either mode, a 'scop classification file' is required as a source of family classification data. A scop classification file contains classification and other data for domains from the scop database. The file is in embl-like format and is generated by scopparse. Domain sequence information can be added to the file by using scopseqs. * -targetf infile A 'scop validation file' contains sequence relatives (hits) for each of a number of different scop families, superfamilies and folds. The file contains the collated results from psiblast searches of a sequence database for the indvidual scop families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a scop superfamily or fold instead. The scop validation file is generated by seqnr and is in embl-like format. * -maxhits integer The maximum number of hits to be written to the signature hits file. * -overlap integer When estimating the statistical significance of scored matches of different types of discriminating element to a sequence, two (or more) p-values are only ever multiplied together if corresponding hit is to the same region of the protein. 'Same' is defined as two hits overlapping by a user-defined number of residues. -mrgoutpath string Location of signature hits / library scan files for merged results (output) -mrgoutextn string Extension for signature hits / library scan files for merged results (output) Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-db" associated qualifiers -sbegin integer Start of each sequence to be used -send integer End of each sequence to be used -sreverse boolean Reverse (if DNA) -sask boolean Ask for begin/end/reverse -snucleotide boolean Sequence is nucleotide -sprotein boolean Sequence is protein -slower boolean Make lower case -supper boolean Make upper case -sformat string Input sequence format -sdbname string Database name -sid string Entryname -ufo string UFO features -fformat string Features format -fopenfile string Features file name 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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-mode | Libscan runs in one of two modes either (i) database search mode or (ii) library screen mode. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top-scoring families) for each one. |
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1 | ||||||
-db | In database search mode libscan scans each discriminating element against a sequence set. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) | Readable set of sequences | Required | ||||||
-[no]grib | Use Gribskov profile | Boolean value Yes/No | Yes | ||||||
-[no]henik | Use Henikoff profile | Boolean value Yes/No | Yes | ||||||
-[no]hmm | Use HMM profile | Boolean value Yes/No | Yes | ||||||
-[no]sig | Use signature | Boolean value Yes/No | Yes | ||||||
-hmmpath | Location of HMM profile files (input) | Any string is accepted | ./ | ||||||
-hmmextn | Extension of HMM profile files (input) | Any string is accepted | .hmm | ||||||
-hmmoutpath | Location of signature hits/library scan files for hmm searches (output) | Any string is accepted | ./ | ||||||
-hmmoutextn | Extension of signature hits/library scan files for hmm searches (output) | Any string is accepted | .hmmout | ||||||
-gbvpath | Location of Gribskov profile files (input) | Any string is accepted | ./ | ||||||
-gbvextn | Extension of Gribskov profile files (input) | Any string is accepted | .gribs | ||||||
-gbvgapo | Gap insertion penalty | Any numeric value | 1.0 | ||||||
-gbvgape | Gap extension penalty | Any numeric value | 1.0 | ||||||
-gbvoutpath | Location of signature hits/library scan files for Gribskov profile searches (output) | Any string is accepted | ./ | ||||||
-gbvoutextn | Extension of signature hits/library scan files for Gribskov profile searches (output) | Any string is accepted | .gribout | ||||||
-hnfpath | Location of Hennikoff profile files (input) | Any string is accepted | ./ | ||||||
-hnfextn | Extension of Hennikoff profile files (input) | Any string is accepted | .henik | ||||||
-hnfgapo | Gap insertion penalty | Any numeric value | 1.0 | ||||||
-hnfgape | Gap extension penalty | Any numeric value | 1.0 | ||||||
-hnfoutpath | Location of signature hits/library scan files for Henikoff profile searches (output) | Any string is accepted | ./ | ||||||
-hnfoutextn | Extension of signature hits/library scan files for Henikoff profile searches (output) | Any string is accepted | .henikout | ||||||
-sigpath | Location of signature files (input) | Any string is accepted | ./ | ||||||
-sigextn | Extension of signature files (input) | Any string is accepted | .sig | ||||||
-nterm | Select number |
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1 | ||||||
-sub | Residue substitution matrix | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||||
-siggapo | Gap insertion penalty | Any numeric value | 10.0 | ||||||
-siggape | Gap extension penalty | Any numeric value | 0.5 | ||||||
-sigoutpath | Location of signature hits/library scan files for signature searches (output) | Any string is accepted | ./ | ||||||
-sigoutextn | Extension for signature hits/library scan files for signature searches (output) | Any string is accepted | .sigout | ||||||
-scopf | In either mode, a 'scop classification file' is required as a source of family classification data. A scop classification file contains classification and other data for domains from the scop database. The file is in embl-like format and is generated by scopparse. Domain sequence information can be added to the file by using scopseqs. | Input file | Required | ||||||
-targetf | A 'scop validation file' contains sequence relatives (hits) for each of a number of different scop families, superfamilies and folds. The file contains the collated results from psiblast searches of a sequence database for the indvidual scop families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a scop superfamily or fold instead. The scop validation file is generated by seqnr and is in embl-like format. | Input file | Required | ||||||
-maxhits | The maximum number of hits to be written to the signature hits file. | Any integer value | 50 | ||||||
-overlap | When estimating the statistical significance of scored matches of different types of discriminating element to a sequence, two (or more) p-values are only ever multiplied together if corresponding hit is to the same region of the protein. 'Same' is defined as two hits overlapping by a user-defined number of residues. | Any integer value | 10 | ||||||
-mrgoutpath | Location of signature hits / library scan files for merged results (output) | Any string is accepted | ./ | ||||||
-mrgoutextn | Extension for signature hits / library scan files for merged results (output) | Any string is accepted | .mrgout | ||||||
Additional (Optional) qualifiers | Allowed values | Default | |||||||
(none) | |||||||||
Advanced (Unprompted) qualifiers | Allowed values | Default | |||||||
(none) |
The format of the scop classification file is described in scopparse
The format of the signature files is explained in siggen
The format of the profile and hmm files is explained in documentation for the propechy application and the hmmer package respectively.
The format of the signature hits file is described in sigscan
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
libscan requires a residue substitution matrix.
Program name | Description |
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contacts | Reads coordinate files and writes files of intra-chain residue-residue contact data |
fraggle | Removes fragment sequences from files of hits for scop families |
hmmgen | Generates a hidden Markov model for each alignment in a directory by using the HMMER package |
interface | Reads coordinate files and writes files of inter-chain residue-residue contact data |
profgen | Generates various profiles for each alignment in a directory |
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 |
scopalign | Generate alignments for families in a scop classification file by using STAMP |
scoprep | Reorder scop classificaiton file so that the representative structure of each family is given first |
scopreso | Removes low resolution domains from a scop classification file |
seqalign | Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments |
seqsearch | Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments |
seqsort | Reads multiple files of hits and writes (i) a scop families file and (ii) a scop ambiguities file |
seqwords | Generate file of hits for scop families by searching swissprot with keywords |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigplot | Generates data files of signature performance |
sigscan | Scans a signature against swissprot and writes a signature hits file |
Hidden Markov models can be generated for scop families by using hmmgen which uses the HMMER package.
Simple frequency matrices, Gribskov profiles and Hennikoff profiles can be generated for scop families by using profgen.
A 'signature file' contains a sparse sequence signature. The files are generated by siggen.
A 'signature hits file' contains the results of a search of a discriminating element (one of protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. The files are generated by sigscan and modelscan.
A 'library scan file' holds the results of a search of a sequence against a library of discriminating elements for scop families (one directory for each type of element, e.g. sparse sequence signatures, profiles or HMMs).
The library scan file contains, for each invividual type of discriminating element and for the combination of the elements, classification and other data for each of a user-defined number of top-scoring families (discriminators) from the scop database.
A 'scop classification file' contains classification and other data for domains from the scop database. The file is in embl-like format and is generated by scopparse. Domain sequence information can be added to the file by using scopseqs.
A 'scop validation file' contains sequence relatives (hits) for each of a number of different scop families, superfamilies and folds. The file contains the collated results from psiblast searches of a sequence database for the indvidual scop families; hits of unambiguous family assignment are listed under their respective family, otherwise a hit is assigned as relatives to a scop superfamily or fold instead. The scop validation file is generated by seqnr and is in embl-like format.
Ranjeeva Ranasinghe (rranasin © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK