Advanced SRS Course 12/12/02

-Linking-Subentries-Applications

Linking in SRS

Types of Links

• Hyperlinks

-links between entries which are displayed as hypertext

-useful for examining entries that are referenced directly from

entries

• Query links

-allow you to construct queries using the relationships between

databanks

-require SRS to search through entries or indices in other

databanks looking for matches

Links between Databases

SWISS-PROT

EMBL

PDB

InterPro

PROSITE

PFAM

BLOCKS

Advantages of SRS Linking

Links are bi-directional

A B C

Direct link from ‘A’ to ‘B’ Direct link from ‘B’ to ‘C’

Multistep link from ‘A’ to ‘C’

Database Network Graph

The link page

• Two forms of the link page:

-type you see if you initiate linking from either the query

manager or the query result page

-type you see if you initiate linking from an individual

entry page

• The difference is at the top of these pages– one provides a “find all entries” option, the other does not

• (see next 2 slides)

From query manager or query result page

Find all entries options• In the selected databanks which are linked to the current query

- this returns entries from other databanks which have links

with entries in the current query

• In the current query which are linked to all selected databanks

- this limits the query so that it includes only the entries(from the

original query) which are linked to all of the selected databanks

• In the current query which are not linked to any of the selected

databanks

- this limits the query so that it includes only the entries(from the

original query) which do not have links to the specified databanks

From an individual entry page

No ‘find all entries’ options available

Linking from query manager page

• Can link from a single query or from multiple queries

• two ways to link your queries from the query manager page:

- tick the checkbox that corresponds to a query set and click

the LINK button

- use the text box beside the Expression button

Expression linking

• Useful alternative to using the linking pages

• Can be used to search for a link between two or more sets

of results or between a set of results and a databank

Linking operators

• < entries in the set or databank to the left of the operator are

returned if they have a link to any entries in the set or databank

to the right of the operator

• > entries in the set or databank to the right of the operator are

returned if they have a link to any entries in the set or databank to

the left of the operator

Linking operations

< Q1 < Q2 In Q1 that link to Q2

> Q1 > Q2 In Q2 that link to Q1

combined with logical operators:

< & Q1<Q2 & Q3 In Q1 that link to Q2 &Q3

< | Q1<Q2 | Q3 In Q1 that link to Q2 or Q3

< ! Q1<Q2 ! Q3 In Q1 that link to Q2

but not Q3

A1A2A3A4A5A6

B1B2B3B4B5

A B

A > B is B2 B3 B4 (all entries in B that have links to A)

A < B is A1 A2 A5 A6 (all entries in A that have links to B)

Subentries

Subentries • Necessary when there is repeated structured

information within an entry

FT DOMAIN 1 12 LUMENAL (POTENTIAL). FT TRANSMEM 13 33 POTENTIAL. FT DOMAIN 34 55 CYTOPLASMIC (POTENTIAL). FT TRANSMEM 56 76 POTENTIAL. FT DOMAIN 77 95 LUMENAL (POTENTIAL).

DR EMBL; L44581; AAA99933.1; -. DR EMBL; L44582; AAA99934.1; -. DR EMBL; L44583; AAA99935.1; -. DR EMBL; L44584; AAA99936.1; -. DR EMBL; L44585; AAA99937.1; -. …..

Use subentries to:

• Search for entries containing one or more subentries with certain values and obtain a list of entry references

• Search for subentries with certain values and obtain a list of subentry references

Subentries have a double function:

• They are part of the entry and often require data from other fields in order for their meaning to be resolved and displayed

• Example: a SWISS-PROT feature requires part of the entry’s sequence to be displayed

• They can be regarded as databanks themselves and can be indexed and queried independently from the entries

• Example: search all the transmembrane segments with a given range of length

Subentries available

• Protein databases have 5 subentries:– Reference

– Comment

– Links

– Feature

– Counter

• Nucleotide databases have 3 subentries:– Reference

– Features

– Counters

Controlled vocabularies

• Some of the fields belonging to the subentries have a predetermined number of keys ( as specified by the database documentation). These fields have a controlled vocabulary and when you use the extended query forms you can select a value from a drop down menu. Examples are:– CommentType– DbName– FtKey– CountItem

The Counter subentry• This is a special subentry created by SRS on the fly.

• It counts the number of times particular feature keys, comment types and links to a certain database occur within an entry

• It can be used to answer questions like:– How many entries have 3 or more links to EMBL?

– How many entries have more than 8 disulphide bridges?

– How many entries have 2 or more comments about function?

Subentry fields

• In the standard query form each subentry field name is preceded by the name of the subentry to which it belongs:

• Reference:authors

• Feature:FtKey

• Links:DbName

• The extended query form is divided up into sections. The top section contains the fields belonging to entry and below this are the subentries and the fields that they contain

Links with sets containing subentries

• Two types:– Simple Links– Parent Links

• It is not possible to combine sets of entries with sets of subentries using the logical operators

but link operators may be used between sets of entries and sets of subentries

[swissprot-org:human] > [swissprot-ftkey:transmem]

gives a set of transmembrane segment subentries found in human proteins

[swissprot-org:human] < [swissprot-ftkey:transmem]

returns all human entries that have a transmembrane segment

Simple links

Parent Links

• Sometimes it is necessary to do an explicit conversion from subentries to entries. This can be done using the operand parent. This method looks for links from the subentries to their respective parent entries and retrieves a set containing parent entries.

[swissprot-ftkey:transmem] > parent

gives the parent entries for the set of subentries from SWISS-PROT that have transmembrane sequence features

• Logical operators can then be used to combine the set of parent entries with another set of entries

Types of entries

Query Form

Using entry…..

Feature that is 10 aa in length

Using feature…..

Only returns transmemregions of exactly 10 aa

Applications

Applications in SRS

SWISSPROT

Upload user owneddata

Sequence

query

Run BLAST

launch

BLAST results- text file

BLAST

Indexing

linking

Pathway

Prosite

Protein Applications in SRS

Homology and similarity tools:BLASTP : database search toolFASTA : database search toolMPSrch

Protein function analysis tools:PPSearh : BLASTProdomScanRegExpFingerPrintScanPfScanInterProScanMPSrch

• Sequence analysis tools: - ClustalW

Nucleotide applications in SRS

Homology and similarity toolsBLASTNNFASTAFASTXFASTY

Sequence analysis tools:NClustalWRestrictionMap