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Documentation DAS alignment service

Retrieve a pairwise or multiple alignment

Version:1.1 - Feb. 03. 2006

Scope: Reference servers.

Command: alignment

Format:

PREFIX/das/alignment?query=ID[&subject=ID[RANGE]][&rows=START-END][&subjectcoordsys=COORDSYS]

Description: This query returns one or all alginments that are available for the query on this.

Arguments:

query (required; one) the id of the query.
subject (optional; one or more) the id of the alignment - subject.
To be able to deal e.g. with large numbers of sequence
alignments it is possible to request an accession code +/- a range
of sequences around this sequence. by providing the optional RANGE

:before,after
where before and after are integers defining a range. e.g
/das/pfam/alignment?query=PF00307&subject=P15498:5,5
rows (optional; one) request a certain range of
alignments, in case of servers that provide multiple alignments.
subjectcoordsys (optional;one) request that the subjects
belong to a particular coordinate system. coordinate systems are
defined at the DAS registration server: To get a list of available alignments for query use the entry_points request.

Response:

The response to the dsn command is the "DASALIGNMENT" XML-formatted document.

Format:

<?xml version="1.0" standalone="no"?>
<!doctype dasalignment system "http://www.biodas.org/dtd/dasalignment.dtd">
<dasalignment>
	<alignment type="type" name="name" description="description" position="position" max="maximum" >
	<alignObject dbAccessionId="someid" objectVersion="version" intObjectId="internalId" type="objectType" dbSource="someSouce" dbVersion="version" dbCoordSys="coords"  >
		<alignObjectDetail dbSource="someSouce" property="property">
			some details about the object. e.g. description, etc. 
		</alignObjectDetail> 
		<sequence>
			SEQUENCESEQUENCESEQUENCE
		</sequence>	
	</alignObject>
	<score methodName="scorename" value="scorevalue">
	<block blockScore="score" blockOrder="position"> 	
		<segment intObjectId="intObjectId" start="start" end="end" orientation="+">
			<cigar>9I5M10D</cigar>
		</segment>
	</block> 	
	<geo3D intObjectId="intObjectId">
		<vector x="xCoord" y="yCoord" z="zCoord"/>
		<matrix 
			   mat11="float" mat21="float" mat31="float" 
			   mat12="float" mat22="float" mat32="float"
			   mat13="float" mat23="float" mat33="float"/>
	</geo3D>	
	</alignment>


</dasalignment>

Example

1a4a alignment PDB - UniProt http://das.sanger.ac.uk/das/msdpdbsp/alignment?query=1a4a

alignment ENSP - uniprot http://das.sanger.ac.uk/das/aliguniprotensp/alignment?query=ENSP00000329399

Element:<!doctype>

(required; one only) >The doctype indicates which formal DTD specification to use. For the dna query, the doctype DTD is "http://www.biodas.org/dtd/dasdna.dtd".

Element:<dasalignment>

(required; one only)

The appropriate doctype and root tag is DASALIGNMENT.

Element:<alignment>

(required; one or more) everything below belongs to an alignment.

attribute:type

(optional) the type of the alignment

attribute:name

(optional) the name of the alignment

attribute:description

(optional) a human readable description of this alignment

attribute:position

(optional) if multiple alignments (or ranges of alignments) are returned, the position of this alignment

attribute:max

(optional) the total number of alignments available. (useful if a range of a multiple alignment is returend).

Element:s<alignObject>

(required; two or more) A description of the objects that are aligned.

attribute:objectVersion

(required) version of Object. e.g. CRC64 checksum for protein sequences.

attribute:intObjectId

(required) internal, unique name name for this object. This is used in the SEGMENT section to identify to which object an alignment belongs to.

attribute:type

(optional) a type for this object.e.g. DNA, PROTEIN, STRUCTURE, etc.

attributeGroup:dbRef

This attribute group is used for referring to a database.

attribute:dbSource

(required). The name of the database.

attribute:dbVersion

(required). The version of the database.

attribute:dbCoordSys

(optional). The co-ordinate system used by the database. This is not always
the same as the database. For example, Pfam uses UniProt as an underlying co-ordinate system.
Coordinate systems are defined at the DAS registration server

attribute:dbAccessionId

(required). The database entry accession id. For example, SCOP have sunid, Pfam accessions(PF01020).

Element:<sequence>

(optional; one) the sequence of this object. Clients generally should use the DAS - SEQUENCE request to get the seqeuence, so this is optional.

Element:<alignObjectDetail>

(optional; zero or more) details about the object

attributeGroup:detail

The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.

attribute:dbSource

(required). The database where the information about this source orginates.

attribute:property

(required). A description of the CDATA. For example, if you wanted to give an alternative id for a database, e.g. a UniProt ID , then the <someDetail dbSource="UniProt" property="id">VAV_HUMAN</someDetail>

Element:<score>

(optional; zero or more) a score for this alignment. an alignment can be described with several scores. each of the scores is described with the following

attributes:

attribute:methodName

(required) the name of the score, e.g. number of equivlanet residues (eqr), e-value, etc.

attribute:value (required) the value of the score e.g. 99, 10e-22 , etc.

Element:<block>

(required; one or more) a block of the alignment. an alignment can consist of one or more blocks. Often it will be only one block, since the CIGAR type of writing the alignment information allows to encode blocks.

attributes:

attribute:blockScore

(optional) some kind of score for a block

attribute:blockOrder

(required) The number of block in the alignment.

Element:<segment>

attributeGroup:region

The following attributes are bundled together to form a group of attributes that are capable of defining a region on something using a predefined co-ordinate system.

attribute:start

(optional). The start co-ordinate.

attribute:end

(optional).The end co-ordinate.

attribute:intObjectId

(required). The internal ID of the object.

attribute:orientation

(optional). Strand of the object

Element:<cigar>

(optional). encoding of the alignment. The "cigar" string provides an efficient way to encode an alignment. 15M2D3I e.g. means that the 15 residues of the sequence are Matched (aligned), then there are 2 Deletions, followed by 3 Insertions. Since in some situations the alignment will just consist of an aligned block, the cigar string is optional. If it is missing the alignment is ungapped and ranges from "start" to "end" of the SEGMENT.

Element:<geo3D>

(optional) geometrical operation on 3D object. if the objects to be aligned are three dimensional objects this section defines how one of the needs to be shifted and rotated in order to be superimposed with the others.

attribute:intObjectId

(required) The internal ID of the object.

Element:<vector>

(required, one) the shift vector the x,y, and z attributes are describing the shift vector.

Element:<matrix>

the "container" for the rotation matrix elements.

attribute:mat11 - mat33

(required) The rotation matrix