Search tips

Source: user can retrieve all sequences belonging to the selected plant.


Sequence identifier:  allows sequence retrieval by Sequence id (i.e. cr12_K14). In this search box it is possible to insert one or more accession numbers separeted by ' ; '.


Accession:  allows sequence retrieval by GenBank Accession number (i.e. EX142501). In this search box it is possible to insert one or more accession numbers separeted by ' ; '.


Library: search by sequence library of origin. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Development stage:  allows sequence retrieval specifying the development stage of origin. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Tissue: allows sequence retrieval specifying the tissue of origin. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Length: user can choose sequence length intervals for sequence retrieval. The Lenght ≥ and the Length ≤ boxes can be filled in independently.


Keyword search: user can perform text search in the annotation field of the resulting BLAST hits. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


E-value: to define search E-value intervals.


Gene Ontology annotation: user can perform text search on the description field of each GO entry. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Gene Ontology accession: allows sequence retrieval specifying the GO accession (i.e. GO:0004365 ). In this search box it is possible to insert one or more GO accessions separeted by ' ; '.


Limit to EST sequences (button active): user can limit the search to sequences which contains vector contaminations (check button on) or which contains low complexity sequences and repeats (check button on).


Limit to ESTs not cleaned from vector contaminations (button active): allows users to retrieve all sequences clean from vector contaminations and containing or not low complexity sequences and repeats. To search all the sequences both the checked buttons must be turned off.


Limit to ESTs: user can limit the query to singlets (check button on) or to sequences which belongs to a contig (check button on). To search all the sequences both the checked buttons must be turned off. Moreover user can limit the query to sequences without BLAST matches (check button on).


The query is case-insensitive.

Source: user can retrieve all clusters identified into the selected plant.


Cluster id: allows cluster retrieval by the identifier assigned by the ParPEST software (i.e. cr.saCl001436). In this search box it is possible to insert one or more identifiers separeted by ' ; '.


# of contigs whitin cluster: user can retrieve all clusters made up of a number of contigs grater or smaller than the specified one.


# of ests whitin cluster: user can retrieve all clusters made up of a number of sequences grater or smaller than the specified one.


Keyword search: user can perform text search in the Annotation field of the resulting BLAST hits. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


E-value: to define search E-value intervals.


Gene Ontology annotation: user can perform text search on the description field of each GO entry. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Gene Ontology accession: allows sequences retrieval specifying the GO accession (i.e. GO:0004365 ). In this search box it is possible to insert one or more GO accessions separeted by ' ; '.


The query is case-insensitive.

Source: user can retrieve all 'Transcript indices' identified into the selected plant.


Development stage : allows 'Transcript indices' sequence retrieval specifying the development stage of origin. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Tissue: allows 'Transcript indices' sequence retrieval specifying the tissue of origin.Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Keyword search: user can perform text search in the Annotation field of the resulting BLAST hits. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Enzyme ID: allows sequences retrieval specifying the Enzyme ID (i.e. 1.2.1.12). In this search box it is possible to insert one or more Enzyme ID separeted by ' ; '.


Gene Ontology annotation: user can perform text search on the description field of each GO entry. Partial words and boolean logic operators ' AND ' and ' OR ' are allowed.


Gene Ontology accession: allows sequences retrieval specifying the GO accession (i.e. GO:0004365 ). In this search box it is possible to insert one or more GO accessions separeted by ' ; '.


KEGG metabolic pathway: allows all 'Transcript indices' sequences retrieval belonging to the selected matabolic pathway.


Limit to Transcripts: user can limit the search to sequences with Enzyme id reference (check button on) or with no Enzyme id reference (check button on), with KEGG map reference (check button on) or with no KEGG map reference (check button on).


The query is case-insensitive.