14
Introduction to Sequence Analysis
Nucleotide Analysis
Interpreting the results of BLAST2 EVEC
¥Underneath the score list, you can view the pairwise alignments of sequences from the score list against your query sequence. Note that matching sequences are connected with a "|" symbol. As this is a perfect match, all of the nucleotides are connected with a "|" symbol, mismatches would be connected with a blank space. A gap would be represented with a "-" symbol. Thus a sequence alignment can be represented in the format:


Score= normalized bits (raw bits)

The score of the alignment, called score or bit score, is the sum of log odds scores of each matching amino acid pair in the alignment less gap penalites; the raw score in bits is also shown in parentheses.
The expect value E (E-value) of chance matches of unrelated sequences from a database of this size and the percent identities in the alignment is shown.