Query sequences

In the protein structure database PDB ( http //www. rcsb.org/pdb), by X-ray crystallography and NMR spectroscopy, experimentally solved 3D-protein structures are available to the public. Homology model building for a query sequence uses protein portions of known 3D-stmctures as structural templates for proteins with high sequence similarity. 

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 final round scores from iterative profile methods do not reflect the real significance of the match to the query sequence. The significance says how likely the protein segment matches to the profile constructed in the previous round. For example, if a false-positive match with an E... 

To identify the relationship between anew gene or the query sequence and those genes that are already known or stored in public databases and to elucidate the functions the new gene may have, programs in BLAST are usually used see Table 1.1). BLAST provides a similarity search for both nucleotide and protein sequences against genomic sequence information available in the databases see Note 3). 

The BLAST searching output can help users deduce functional and evolutionary information for their query sequences. BLAST can also be used for comparisons in certain categories, such as SNP BLAST and Immunoglobin BLAST (IgBlast). 

Programs for the prediction of 3-D stracture usually use available protein domains from PDB see Table 1.1) as templates. Tools that are nsually used include SWISS-MODEL see Table 1.1). The query result includes the template used, the ahgnment between the query sequence and the template, and the predicted 3-D model. 

At the result page, the query sequence is displayed with TMH regions in red, when the query GPGR belongs to Class A family. 

Every hit in the list is aligned to the query sequence and is revealed below the hit list (not shown). 

Computational analyses of DNA sequences/gene identification can be carried out by the use of Internet resources. Because no single tool can perform all the relevant sequence analysis leading to gene identification, it is recommended to submit the query sequence to the analysis of several software packages to make use of the best... 

Sequence similarity search tools Alignments of the query sequence with databases produce sequence similarity. The BLAST series of programs has variants that will translate DNA databases, translate the input sequence, or both. FASTA provides a similar suite of programs. 

The SPL (search for potential splice sites) tool of the Sanger Centre predicts splice sites of an input query sequence. On the nucleotide sequence analysis page, paste the query sequence, enter the sequence name, select SPL tool, and click the... 

Figure 10.8. Gene identification by Procrustes. The nucleotide sequence encoding human lysozyme is used as a query sequence to identify its gene structure against known protein sequence (i.e., pig lysozyme protein). The output includes sequence aignment of the source (predicted translate) versus target protein (pig lysozyme).

---