PyMood BLAST Launcher Setup NCBI BLAST Setup Parameters

BLAST type: Any of the standard NCBI BLAST types may be selected in this window. They are blastp, blastn, blastx, tblastn, tblastx. Please refer to http://www.ncbi.nih.gov/blast/ for the descriptions.

# of hits: Any positive integer may be typed here. This number will reflect the maximum number of hits shown in the BLAST output file for every query sequence.

# of align: Any positive integer may be typed here. This number will reflect the maximum number of aligned sequences in the BLAST output file. However, for visualization of the BLAST output data, PyMood BLAST parser will only use the alignment with the best expectation (e) value.

Expect value is the cutoff expectation value. Sequences with lower homology (higher number for expectation value) than this number will not be shown in the BLAST output file, in the PyMood Canvas, and in the annotation files. Any positive number may be typed here. The default cutoff expectation value is 1e-8.

Matrix: Protein BLAST and translated BLAST programs, blastp, blastx, tblastn, and tblastx require a substitution matrix. Any of the standard matrices may be selected in this window. The matrices are: BLOSSUM62, BLOSSUM45, BLOSSUM80, PAM30, AND PAM70. The default matrix is BLOSSUM62.

Filter (on/off): 'On' will switch on the normal BLAST2 filtering, and 'off' will switch off the filtering.

Query database genetic code: The number '1' is the standard genetic code. Any number corresponding to another genetic code embedded into NCBI BLAST2 may be selected in this window.

Target database genetic code: The number '1' is the standard genetic code. Any number corresponding to another genetic code embedded into NCBI BLAST2 may be selected in this window.