Translated BLAST ( BLASTX ) - runs an input DNA sequence againnst the protein databases. Simple Is Beautiful is a novel methodology that aims to improve the statistical assessment of hits returned from a PSI-BLAST search to yield better delineation of true and false positives.( Reference: Lee, M.M. et al. Since interpretation of the results requires scientific tact you might want to check the potential homologs using SIB-BLAST. NCBI provides a PSI-BLAST tutorial, and a YouTube video.
If you suspect that your pprotein may only show weak sequence similarity to other proteins, I would suggest clicking on the PSI-BLAST (Position-Specific Iterated BLAST) feature. This program is also coupled with a motif search. the default database is the "nucleotide collection (nt/nr)." Comparatively recently NCBI offers the ability to conduct Batch BLAST searches. In BLASTX your nucleotide sequence will be translated in all six reading frames and the products compared with the nr protein database. Several online tutorial are available including BLAST QuickStart and Basic Web BLAST from NCBI and a YouTube video. BLASTP will compare your protein sequence with all the protein sequences in nr. BLASTN will compare your DNA sequence with all the DNA sequences in the nonredundant database (nr). BLAST (Basic Local Alignment Search Tool) & FASTAīACKGROUND INFORMATION : The three BLAST programs that one will commonly use are BLASTN, BLASTP and BLASTX.
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