Word size
|
Any word size for any program mode. Neighborhood words are turned off
for word sizes of 5 or greater, but may be activated by setting an
explicit value for T.
|
blastn has a minimum word size of 7.
blastp, blastx,
tblastn, and tblastx have
word sizes of 2 or 3. Neighborhood words are never used for
blastn.
|
Nucleotide scoring
|
Choice of match/mismatch or scoring matrix.
|
Only match/mismatch scoring.
|
Nucleotide statistics
|
Karlin-Altschul parameters are available for several match/mismatch
values and gap costs.
|
Karlin-Altschul parameters are always computed without respect to gap
costs. Reported E-values may greatly overestimate significance.
|
altscore
|
Allows score modification for any matrix (e.g., to set stop scores
lower).
|
Nothing similar.
|
H, K, L,
gapH, gapK,
gapL
|
Especially useful when using unsupported scoring schemes; allow the
provision of values for Karlin-Altschul parameters.
|
Nothing similar. Unsupported scoring schemes are fatal errors.
|
Alias databases
|
No, but virtual databases offer similar functionality.
|
Yes, both alias and virtual databases are supported.
|
Gapped alignment
|
All programs.
|
All programs except tblastx.
|
/etc/sysblast
|
Allows systems administrators to set system-wide resource
restrictions.
|
Nothing similar.
|
Database subset selection
|
Yes, via dbrecmin and dbrecmax.
|
No, but alias databases can be used for static splitting.
|
Restricted region of query
|
The nwstart and nwlen
parameters restrict seeding but not alignment.
|
-L restricts both seeding and alignment.
|
links
|
Displays the order of alignments in a group.
|
Nothing similar.
|
topcomboN
|
Allows restriction of number alignment groups. Groups are clearly
labeled.
|
Nothing similar.
|
kap
|
Computes significance without sum statistics.
|
Nothing similar.
|
olf, golf,
olmax, golmax
|
Allows setting of overlap rules for HSP consistency.
|
Fixed internally.
|
notes, warnings,
errors
|
Descriptive messages at various levels ofcaution.
|
Most error messages are terse and not user friendly.
|
Output formats
|
Only the standard format.
|
Multiple output report formats including HTML, ASN.1, XML, tabular,
and anchored multiple alignments. See Appendix A.
|