Introduction to sequence alignment  (Page 3/4)

The third section of the results page contains the actual alignments, listed in the same order as the graphed results and the scores.

Look for entry with the accession code BC005255.1 at the beginning of the alignment and click on the accession link. Note that this "hit" is a cDNA, or a DNA sequence that has been copied from anmRNA molecule by the enzyme reverse transcriptase. This is indicated in the description, but whenever the source of the sequenceis unclear, click the link for the GI number and view the GenBank entry for more information. Look under the "COMMENT" section foradditional details about this sequence.

Return to the BLAST alignment results page. Scroll down to view the actual sequence alignments. The alignments are represented with vertical lines illustrating identicalmatches, blanks indicate no match. In these nucleotide alignments, there is no measurement for similarity between non-identical nucleotides. In protein alignments, however, chemical or structural similarity isusually identified between the amino acids.

Return to the BLAST home page , and select the blastx "translated nucleotide sequence query". Cut and paste the same nucleotide sequence used in theprevious example into the "Search" box. The default translation tool is BLASTX, which translates the query sequence into a protein sequence and searches a protein database. To search a translatednucleotide database with a protein query, the TBLASTN algorithm should be selected. To search a translated nucleotide database with a translated nucleotide sequence, the choice would be TBLASTX. TBLASTXis the most computationally intensive of these three searches, therefore common practice is to use BLASTX first to search protein sequence databases, and then if there are no hits withBLASTX, consider TBLASTX to translate nucleotide sequence database entries into protein sequences. For this example, use the translation algorithm BLASTX. Use the nr database and leave the default values for all other BLAST options, and hit BLAST.View the results page.

Look at the first alignment, which should have 100% identitybetween the aligned subsequences. Note that a particular alignment may have more than one sequence associated with it. Therefore, you must look at the actual alignments, not the list of scores, to answer the following questions.