embsig

Data type AjPSigpos

Ajax Sigpos object.

Holds data for compiled signature position

AjPSigpos is implemented as a pointer to a C data structure.

Alias name(s)

Name Description

AjSSigpos

AjOSigpos

Name	Description
AjSSigpos
AjOSigpos

Attributes

Name Type Description

ngaps No. of gaps

gsiz Gap sizes

gpen Gap penalties

subs Residue match values

Name	Type	Description
ngaps	No. of gaps
gsiz	Gap sizes
gpen	Gap penalties
subs	Residue match values

Constructor(s)

Name Description

embSigposNew Default Sigdat object constructor

Name	Description
embSigposNew	Default Sigdat object constructor

Destructor(s)

Name Description

embSigposDel Default Sigdat object destructor

Name	Description
embSigposDel	Default Sigdat object destructor

Data type AjPSigdat

Ajax Sigdat object.

Holds empirical data for an (uncompiled) signature position. Important: Functions which manipulate this structure rely on the data in the gap arrays (gsiz and grfq) being filled in order of increasing gap size.

AjPSigdat is implemented as a pointer to a C data structure.

Alias name(s)

Name Description

AjSSigdat

AjOSigdat

Name	Description
AjSSigdat
AjOSigdat

Attributes

Name Type Description

nres No. diff. types of residue

rids Residue id's

rfrq Residue frequencies

nenv No. diff. types of environment

eids Environment id's

efrq Environment frequencies

ngap No. diff. sizes of empirical gap

gsiz Gap sizes

gfrq Frequencies of gaps of each size

wsiz Window size for this gap

Name	Type	Description
nres	No. diff. types of residue
rids	Residue id's
rfrq	Residue frequencies
nenv	No. diff. types of environment
eids	Environment id's
efrq	Environment frequencies
ngap	No. diff. sizes of empirical gap
gsiz	Gap sizes
gfrq	Frequencies of gaps of each size
wsiz	Window size for this gap

Constructor(s)

Name Description

embSigdatNew Default Sigdat object constructor

Name	Description
embSigdatNew	Default Sigdat object constructor

Destructor(s)

Name Description

embSigdatDel Default Sigdat object destructor

Name	Description
embSigdatDel	Default Sigdat object destructor

Data type AjPSignature

Ajax Signature object.

AjPSignature is implemented as a pointer to a C data structure.

Alias name(s)

Name Description

AjSSignature

AjOSignature

Name	Description
AjSSignature
AjOSignature

Attributes

Name Type Description

Type Type, either ajSCOP (1) or ajCATH (2) for domain signatures, or ajLIGAND (3) for ligand signatures.

Typesig Type, either aj1D (1) or aj3D (2) for sequence or structure-based signatures respectively.

Class SCOP classification.

Architecture CATH classification.

Topology CATH classification.

Fold SCOP classification.

Superfamily SCOP classification.

Family SCOP classification.

Sunid_Family SCOP sunid for family.

npos No. of signature positions.

pos Array of derived data for puropses of alignment.

dat Array of empirical data.

Id Protein id code.

Domid Domain id code.

Ligid Ligand id code.

Desc Description of ligand (ajLIGAND only)

ns No. of sites (ajLIGAND only)

sn Site number (ajLIGAND only)

np No. of patches (ajLIGAND only)

pn Patch number (ajLIGAND only)

minpatch Max. patch size (residues) (ajLIGAND only)

maxgap Min. gap distance (residues) (ajLIGAND only)

Name	Type	Description
Type	Type, either ajSCOP (1) or ajCATH (2) for domain signatures, or ajLIGAND (3) for ligand signatures.
Typesig	Type, either aj1D (1) or aj3D (2) for sequence or structure-based signatures respectively.
Class	SCOP classification.
Architecture	CATH classification.
Topology	CATH classification.
Fold	SCOP classification.
Superfamily	SCOP classification.
Family	SCOP classification.
Sunid_Family	SCOP sunid for family.
npos	No. of signature positions.
pos	Array of derived data for puropses of alignment.
dat	Array of empirical data.
Id	Protein id code.
Domid	Domain id code.
Ligid	Ligand id code.
Desc	Description of ligand (ajLIGAND only)
ns	No. of sites (ajLIGAND only)
sn	Site number (ajLIGAND only)
np	No. of patches (ajLIGAND only)
pn	Patch number (ajLIGAND only)
minpatch	Max. patch size (residues) (ajLIGAND only)
maxgap	Min. gap distance (residues) (ajLIGAND only)

Constructor(s)

Name Description

embSignatureNew Default Signature constructor

Name	Description
embSignatureNew	Default Signature constructor

Destructor(s)

Name Description

embSignatureDel Default Signature destructor

Name	Description
embSignatureDel	Default Signature destructor

Output

Name Description

embSignatureWrite Write signature to file.

Name	Description
embSignatureWrite	Write signature to file.

Input

Name Description

embSignatureReadNew Construct a Signature object from reading a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Name	Description
embSignatureReadNew	Construct a Signature object from reading a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Output

Name Description

embSignatureWrite Write a Signature object to a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Name	Description
embSignatureWrite	Write a Signature object to a file in embl-like format (see documentation for the DOMAINATRIX "sigscan" application).

Input

Name Description

embSignatureHitsRead Construct a Hitlist object from reading a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Name	Description
embSignatureHitsRead	Construct a Hitlist object from reading a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Output

Name Description

embSignatureHitsWrite Writes a list of Hit objects to a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Name	Description
embSignatureHitsWrite	Writes a list of Hit objects to a signature hits file (see documentation for the DOMAINATRIX "sigscan" application).

Modifier(s)

Name Description

embSignatureCompile Compiles a Signature object. The signature must first have been allocated by using the embSignatureNew function.

Name	Description
embSignatureCompile	Compiles a Signature object. The signature must first have been allocated by using the embSignatureNew function.

Operator(s)

Name Description

embSignatureAlignSeq Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling embSignatureCompile. Write a Hit object with the result.

embSignatureAlignSeqall Performs an alignment of a signature to protein sequences. The signature must have first been compiled by calling embSignatureCompile. Write a list of Hit objects with the result.

Name	Description
embSignatureAlignSeq	Performs an alignment of a signature to a protein sequence. The signature must have first been compiled by calling embSignatureCompile. Write a Hit object with the result.
embSignatureAlignSeqall	Performs an alignment of a signature to protein sequences. The signature must have first been compiled by calling embSignatureCompile. Write a list of Hit objects with the result.

Data type AjPHit

Ajax hit object.

Holds data associated with a protein / domain sequence that is generated and or manipulated by the EMBOSS applications seqsearch, seqsort, and sigscan.

AjPHit is implemented as a pointer to a C data structure.

Alias name(s)

Name Description

AjSHit

AjOHit

Name	Description
AjSHit
AjOHit

Attributes

Name Type Description

Seq Sequence as string.

Start Start of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.

End End of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.

Acc Accession number of sequence entry.

Spr Swissprot code of sequence entry.

Dom SCOP or CATH database identifier code of entry.

Rank Rank order of hit

Score Score of hit

Eval E-value of hit

Pval p-value of hit

Typeobj Primary (objective) classification of hit.

Typesbj Secondary (subjective) classification of hit

Model String for model type if used, one of PSIBLAST, HMMER, SAM, SPARSE, HENIKOFF or GRIBSKOV

Alg Alignment, e.g. of a signature to the sequence

Group Grouping of hit, e.g. 'REDUNDANT' or 'NON_REDUNDANT'

Target Used for garbage collection.

Target2 Also used for garbage collection.

Priority Also used for garbage collection.

Sig Pointer to signature object for which hit was generated. Used as a pointer only - memory is never freed or allocated to it.

Name	Type	Description
Seq	Sequence as string.
Start	Start of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.
End	End of sequence or signature alignment relative to full length swissprot sequence, this is an index so starts at 0.
Acc	Accession number of sequence entry.
Spr	Swissprot code of sequence entry.
Dom	SCOP or CATH database identifier code of entry.
Rank	Rank order of hit
Score	Score of hit
Eval	E-value of hit
Pval	p-value of hit
Typeobj	Primary (objective) classification of hit.
Typesbj	Secondary (subjective) classification of hit
Model	String for model type if used, one of PSIBLAST, HMMER, SAM, SPARSE, HENIKOFF or GRIBSKOV
Alg	Alignment, e.g. of a signature to the sequence
Group	Grouping of hit, e.g. 'REDUNDANT' or 'NON_REDUNDANT'
Target	Used for garbage collection.
Target2	Also used for garbage collection.
Priority	Also used for garbage collection.
Sig	Pointer to signature object for which hit was generated. Used as a pointer only - memory is never freed or allocated to it.

Constructor(s)

Name Description

embHitNew Default Hit constructor

embHitReadFasta Construct Hit object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitNew	Default Hit constructor
embHitReadFasta	Construct Hit object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Destructor(s)

Name Description

embHitDel Default Hit destructor

Name	Description
embHitDel	Default Hit destructor

Assignment(s)

Name Description

embHitMerge Create new Hit from merging two Hit objects

Name	Description
embHitMerge	Create new Hit from merging two Hit objects

Operator(s)

Name Description

embMatchScore Sort Hit objects by Score element.

embMatchinvScore Sort (inverted order) Hit objects by Score element.

embMatchLigid Sort Hit objects by Ligid element in Sig element.

embMatch Sort Hit objects by Ligid element in Sig element.

embHitsOverlap Checks for overlap between two Hit objects.

Name	Description
embMatchScore	Sort Hit objects by Score element.
embMatchinvScore	Sort (inverted order) Hit objects by Score element.
embMatchLigid	Sort Hit objects by Ligid element in Sig element.
embMatch	Sort Hit objects by Ligid element in Sig element.
embHitsOverlap	Checks for overlap between two Hit objects.

Data type AjPHitlist

Ajax hitlist object.

Holds an array of hit structures and associated SCOP classification records.

AjPHitlist is implemented as a pointer to a C data structure.

Alias name(s)

Name Description

AjSHitlist

AjOHitlist

Name	Description
AjSHitlist
AjOHitlist

Attributes

Name Type Description

Type Domain type, either ajSCOP (1) or ajCATH (2).

Class SCOP classification.

Architecture CATH classification.

Topology CATH classification.

Fold SCOP classification.

Superfamily SCOP classification.

Family SCOP classification.

Model SCOP classification.

Sunid_Family SCOP sunid for family.

Priority True if the Hitlist is high priority.

N No. of hits.

hits Array of hits.

Name	Type	Description
Type	Domain type, either ajSCOP (1) or ajCATH (2).
Class	SCOP classification.
Architecture	CATH classification.
Topology	CATH classification.
Fold	SCOP classification.
Superfamily	SCOP classification.
Family	SCOP classification.
Model	SCOP classification.
Sunid_Family	SCOP sunid for family.
Priority	True if the Hitlist is high priority.
N	No. of hits.
hits	Array of hits.

Constructor(s)

Name Description

embHitlistNew Default Hitlist constructor

Name	Description
embHitlistNew	Default Hitlist constructor

Destructor(s)

Name Description

embHitlistDel Default Hitlist destructor

Name	Description
embHitlistDel	Default Hitlist destructor

Operator(s)

Name Description

embHitlistMatchFold Sort Hitlist objects by Fold element

Name	Description
embHitlistMatchFold	Sort Hitlist objects by Fold element

Input

Name Description

embHitlistRead Construct Hitlist object from reading the next entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitlistRead	Construct Hitlist object from reading the next entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Constructor(s)

Name Description

embHitlistReadFasta Construct Hitlist object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitlistReadFasta	Construct Hitlist object from reading the next entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Input

Name Description

embHitlistReadNode Construct Hitlist object from reading a specific entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitlistReadNode	Construct Hitlist object from reading a specific entry from a file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

Constructor(s)

Name Description

embHitlistReadNodeFasta Construct Hitlist object from reading a specific entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitlistReadNodeFasta	Construct Hitlist object from reading a specific entry from a file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Output

Name Description

embHitlistWrite Write Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistWriteSubset Write a subset of a Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistWriteFasta Write Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistWriteSubsetFasta Write a subset of a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

embHitlistWriteHitFasta Write a single Hit from a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Name	Description
embHitlistWrite	Write Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteSubset	Write a subset of a Hitlist to file in embl-like format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteFasta	Write Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteSubsetFasta	Write a subset of a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).
embHitlistWriteHitFasta	Write a single Hit from a Hitlist to file in extended FASTA format (see documentation for the DOMAINATRIX "seqsearch" application).

Operator(s)

Name Description

embHitlistClassify Classifies a list of signature-sequence hits (held in a Hitlist object) according to list of target sequences (a list of Hitlist objects).