The protein of interest can be found within the XML file by searching with the sequence identifier given in Additional file 1.
The term data integration has also been used as a synonym for data merging in which different data sets are concatenated at the database level by cross-referencing the sequence identifiers, which requires semantic compatibility among data sets [ 25, 26].
Select the database sequence identifier type to be displayed (by default QuickGO displays UniProtKB accessions, e.g. P12345).
As a first step, compression of data was achieved by merging of identical sequence reads and encoding their frequency into the respective sequence identifier.
To find actual sequences search corresponding sequencing centre internet site with the protein sequence identifier.
The reverse sequences were first reverse-complemented and then concatenated with the corresponding forward sequence by mean of a sequence identifier common to the two mate pair sequences.
Singleton sequences are identified by sequence identifiers for SRA003728, with the size (in bp) and quality (% identity) of the alignment between the 454 sequence and the Sanger sequence.
Notably, among the 9673 HPRD identifiers involved in PPIs, 119 were identified to correspond to obsolete nucleotide sequence identifiers, 4 corresponded to non protein-coding RNAs, while 16 were replaced by new nucleotide sequence identifiers; due to this updating, in three cases, two HPRD identifiers were assigned to the same nucleotide sequence identifier.
The web interface to the database is not just a collection of simple tables showing the data, or a simple query to search by using sequence identifiers or keywords.
However, there is no immediate way to match the respective sequence identifiers listed by either RefSeq or Genome Reviews for the same gene of the same reannotated genome, although the knowledgebase UniProt [ 11] began to add links to both genome databases as this paper was in preparation.
