HOW TO SEARCH and QUERY RuphiBase

RuphiBase is the Ruditapes philippinarum transcriptome databases.
The database entries correspond to putative Ruditapes trascripts, chracterised by bioinformatic analyses.
Individual transcripts are associated to different kinds of sequence and annotation by similarity information.
See a sample RuphiBase entry
http://compgen.bio.unipd.it/ruphibase/contig/ruditapes2_c481/

HOW TO SEARCH RuphiBase

The database is searchable form the search page using keywords on all entry fields.
The result of such a search is a table listing accession numbers and descriptions of matching entries, linked to contig pages.
Screenshots of search form, results table and linked entry:

HOW TO BROWSE RuphiBase for MASSIVE DATA RETRIEVAL

The database in browsable: by combining searches of specific keywords in given entry fields the user can retrieve information about all the matching entries, as table separated values (TSV) text files. The special keywors “HAS” can be used to retrieve all the entries with a non empty content of one or more specific fields.
Indeed, the the user can customise the retrieved information.

Simple query:

using a given contig accession number
retrieving contig description and sequence information

ruditapes_c989	casein kinase gamma 3	GTCGGGAAACCGGCCGGCCATTTGGTGTTTGGGTAACCCCGGGGA...

Advanced query:

Using “growth” as keywords on description field
using HAS on GO descriptions, to consider all the entries corresponding to contigs associated to GO terms
etrieving both sequence and annotation information

ruditapes_c28116	growth arrest-specific 8	GO:0008285,GO:0005929,GO:0005794,GO:0009434,GO:0005515,GO:0030317,GO:0005874	GGAAGACGCATGGAGAACAAATGGCTGANATCTCAGCCAAAAATAAAATGCTGGCTGAACCACTACAGAAAGCCCAGGAGGAG...

ruditapes2_c2387	fibroblast growth factor receptor 2	GO:0044425,GO:0004713,GO:0006468,GO:0005886,GO:0005515,GO:0048522,GO:0050793,GO:0048513,GO:0007243,GO:0048869,GO:0004872	AAGGAATGGAATATCTTGCTGGAAGAGGGAT...

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