Functional annotations

Set the task of discovering new, previously unknown druggable receptors, how would we go about it In particular, how would we find a GPCR The first step toward functional annotation of a new GPCR sequence usually involves searching a primary sequence database with pairwise similarity tools. Such searches can reveal clear similarities between the query sequence... 

The second postprocessing step is the automated enhancement of the TrEMBL annotation to bring TrEMBL entries closer to SWISS-PROT standard. There is an increasing need for reliable automatic functional annotation to cope with the rapidly increasing amount of sequence data. Most of the current approaches are still based on sequence similarity searches against known proteins. Some groups try to collect the results of different prediction tools in a simple way, e.g., PEDANT (Frishman and Mewes, 1997) or GeneQuiz (Scharf et al., 1994). However, several pitfalls of these methods have been reported (Bork and Koonin, 1998). 

Fig. 2. Functional annotation of protein B from sequence similarities to protein A. The correct annotation lies above the dotted line. Incorrect cases lie below the dotted line. Objects colored in red indicate errors in annotation. Similar shading of objects...

Comparison of protein active site structures for functional annotation of proteins and drug design. Proteins 65 124-135... 

Lapidus, A. Galleron, N. Sorokin, A. Ehrlich, S.D. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region. Microbiology, 143, 3431-3441 (1997)... 

Brown, S. D., Chambon, P. and de Ange-lis, M. H. (2005) EMPReSS standardized phenotype screens for functional annotation of the mouse genome. Nat Genet 37, 1155. 

As a general trend, de novo transcriptome assembly studies reveal greater transcriptome complexity than expected and provide a blueprint for further studies. De novo transcriptome assembly of black pepper is a representative example of the application of SOLiD RNA-Seq technology in nonmodel species (29). In that study, 71 million short reads, representing a sequencing coverage per base (depth) of 62X, were used to assemble a total of 22,363 transcripts in root samples. Transcript and functional annotation was performed based on the sequence homology with other species. 

In addition to automated functional annotation of putative 5-HT receptor sequences, determination of open reading frames (ORFs), start codons, and intron/exon boundaries from genomic sequences is now also automated. The absence of expert human curation in such automated annotation can potentially lead to the presence of incorrect sequence data in the databases that has arisen from misidentification of ORFs, start codons, and intron/exon boundaries in raw genomic sequences. For example, the sequences of several chimpanzee 5-HT receptors have recently been added to the GenBank databases, but the sequences given for these receptors indicate that one or several of the seven transmembrane (TM) helices are not present in the sequence, although... 

Barglow KT, Cravatt BF (2007) Activity-based protein profiling for the functional annotation of enzymes. Nat Methods 4 822-827... 

Microbiota-Associated Databases (Integrate Functional Annotation Data with Comparative Genome Analysis)... 

Use functional annotation databases to provide insights into the putative functions of the selected genes and gene families and analyze the target structures for possible binding sites, active sites, and other functionally important domains. 

Many databases provide information on functional annotation of the genomes of organisms. One such high-quality standard database is Pfam (19). Pfam is fundamentally a protein domain family database derived based on sequence similarity. Pfam provides details on the functional properties of protein domains of known function. Out of 1,590, 1,495, and 1,536 proteins encoded in the genomes of 26695, J99, and HPAG1 strains of H. pylori, respectively, 1,113, 1,130, and 1,143 proteins have at least 1 protein domain associated (defined by Pfam) with the amino acid sequence. Therefore, for these domains of H. pylori proteins, preliminary indication of their functions is available. 

Kreienkamp HJ, Larusson HJ, Witte I, et al. Functional annotation of two orphan G-protein-coupled receptors, Drostarl and -2, from Drosophila mela-nogaster and their ligands by reverse pharmacology. J Biol Chem 2002 277 39937-39943. 

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