A standard BLAST report has four parts (see Figure 6-1).
The first line contains the name of the program, its version, and its build date. If BLAST crashes or has some kind of unexpected behavior, include this information when you report the problem to the authors. The next piece of information is a reference to the scientific literature, which should be cited if you publish research that employed BLAST. The most important information in the header, the names of the query sequence and the database, appear next. The last line is a progress meter that is updated during the search.
Each line indicates the name of the sequence, the highest scoring alignment found and the lowest E-value for any HSP or group of HSPs. The one-line summaries are often hyperlinked to the alignments farther below when the output comes from a web page. If you just want to know for example, the names of the top matches, these one-line summaries are convenient.
The alignments usually make up the bulk of the report. Figure 6-1 shows only one alignment. The following section discusses alignments in greater detail and gives examples from the five standard BLAST programs.
The footer reports search parameters and various other statistics. The most important features are the word size (W), neighborhood word threshold score (T), Expect (E), and the scoring scheme (scoring matrix or match/mismatch values and the gap costs) because these factors control the sensitivity and specificity of a search. The footer labels these values clearly.