FastA Output

An Example of the FastA histogram is shown below:

  

Figure 5.3: An example of the histogram in FastA Output

The X axis is the score,growing from top to bottom and printed on the left column . The y axis shows the number of matching database records having the score. The observed distribution of the score is plotted by bars of ``='' signs and printed in second column. The expected random distribution of the score is plotted by ``*'' signs and printed on the third column. For example, a score of 34 was attained by 1045 sequences when the query was searched, compared to 1564 expected sequences with a random sequence search. This difference is visible at the corresponding histogram line: the '*' is not at the top of the '=' bar. Note, that on the bottom right a zoom is plotted, providing a closer look at the significant region.
following the graphic output of FastA.

  

Figure 5.4: FastA output: The first lines contain general information about the search parameters. Score lines are made of nine rows: 1-3 details the name and the annotation of the hit, 4-9 are the FastA scores.

Each Line describes one database sequence matching the query, printed in decreasing order of statistical significance. Each contains the name of the record, its database ID, a short description of it, the sequence length and the five FastA scores. Although the statistical significance of a result can be evaluated directly from the E-score and Z-score, interpreting the row scores ( init₁, init_n and opt)may be useful:

• When $init_1 = init_n = opt there is 100 \%$ homology over the matched stretch.
• When init_n > init₁ more than one matching region was found in the database sequence with poorly matching separating regions.
• When opt > init_n the matching regions are greatly improved by adding gaps in one or both of the sequences.