GO offers substantial coverage of major protein databases and provides a species-specific, structured set of terms describing gene products.
We first performed an unconstrained annotation of the transcriptome (Fig. 2) using three major protein databases: nr, SwissProt and TrEMBL.
The size distribution of the contigs is shown in Figure 1.> The unique sequences were compared with the NCBI non-redundant nucleotide database (Nt) and three major protein databases (KEGG, Nr, and UniProt) using the BLASTN and BLASTX algorithms with an E-value cutoff of < 10−5.
To facilitate consistency in protein annotation, UniProt was launched in cooperation with three major protein sequence databases: Swiss-Prot, TrEMBL and PIR [ 24].
One MA is defined by major protein domain databases as a 200-amino acid (aa) motif (Interpro: IPR010629, PFAM: PF06757, Ins_allergen_rp).
Some of the major protein interaction databases (19 25) are now federated in the International Molecular Exchange (IMEx) consortium, whose primary goals are to minimize curation redundancy and to share the data in a common format.
Here, we downloaded the human PPI data from the Protein Interaction Network Analysis PINAA) platform (May 21 , 2014 [ 36], which collected and annotated data from six major protein interaction databases, that is, IntAct, BioGRID, MINT, DIP, HPRD, and MIPS/MPact.
Then, they were compared with sequences in the two major public protein databases (Methods) using the BLASTX algorithm.
All unique assembled sequences (unigenes) were sequentially compared using blast (cutoff e value of 1e-20) withethe sequences in three major public protein databases, prioritizing handmade annotation databases.
All unique sequences were first compared with the sequences in the non-redundant database (Nt) of the NCBI using the BLASTN algorithm and were then compared with the sequences in the three major public protein databases (listed in the Methods section) using the BLASTX algorithm.
