BLAST

From Proteinfunction.net

BLAST ( Basic Local Alignment Search Tool ) finds the region of local similarity between sequences. NCBI-BLAST

BLAST for protein function prediction

Lots of protein function prediction methods take BLAST as a basic sequence database searching tool. The first step of protein function prediction is to limit the large size of protein sequence space to homologous sequences.

Craig E Jones[1] et al reported the protein function prediction using only BLAST . In the article, they found that using more than top 5 blast hit is not helpful for further increase in function annotation accuracy. And simple function annotation ( here GO term is used for function annotation) with the best blast matched sequence is most accurate way of protein function prediction.
 

References

1. Craig E Jones et al, Automated methods of predicting the function of biological sequences using GO and BLAST, BMC Bioinformatics 2005, 6:272
   
2. Debnath Pal et al, Inference of protein function from protein structure, Structure, 2005, 13, 121
3. Richard A. George et al, Effective function annotation through catalytic residue conservation, PNAS, 10,1073
   
4. James C. Whisstock et al, Prediction of protein function from protein sequence and structure, Quarterly Reviews of Biophysics, 36, 307