Table 3. Options and parameter settings available on the BLAST server
| Parameter | Range of choices or values | Function |
|---|---|---|
| Limit by Entrez query Filter (low complexity) |
Yes or no | As used to limit Entrez query restricts databases search |
| Yes or no | Either apply filter or not; removes regions of low sequence; can apply selectively Complexity or human repeats |
|
| Word size | 2-3 proteins, 7-17 nucleotides |
Lower number increases sensitivity; higher number increases speed |
| Descriptions | 0-500 | Number of matching sequences to report |
| Alignments | 0-500 | Number of alignments to show |
| Expect value (E) | 0.001-1000 | Number of matches from unrelated sequences expected by chance from the selected database; smaller values decrease chance of reporting of such matches |
| Genetic code | Various codons | For translation of nucleic acid sequence; use tablesa |
| Graphical | Various choices | Useful display of matches to the sequence query overview; mouse may be used to show alignment |
| Advanced options | - | Type into space providedb |
| aCodon tables include standard, vertebrate mitochondrial, yeast mitochondrial, mold mitochondrial, invertebrate mitochondrial, ciliate nuclear, echinoderm mitochondrial, euplotid nuclear, bacterial, alternative yeast nuclear, ascidian mitochondrial, flatworm mitochondrial, and blepharisma macronuclear. These are numbered for e-mail access. | ||
| bOptions include (where n is an integer 0,1,2, . . . ): G n, penalty or cost to open a gap; E n, penalty to extend a gap; q n, penalty for a mismatch in BLASTN; r n, match score in BLASTN; W n, initial word size; v n, number of descriptions; b n, number of alignments to show; and E r, expect value, where r is a real number such as 10.0. For example, to set the gap opening penalty to 10 and the gap extension penalty to 2, click the mouse on the advanced options form and then type G 10 E 2. For more advanced searches of the entire proteome of an organism using stand-alone BLAST on a local machine, additional options must be used, e.g., effective database size, to obtain reliable statistical results. | ||
