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Basic Local Alignment Search Tool.
Command line BLAST - blastall
Information that blastall requires:
- the query sequence name
- the database name
- the "flavour" of the blast search you want to run
- although optional, it is a very good idea to give blastall the name of a file to put all
the output into so that you can find it easily later on.
As with any version of blast, the databases to be searched must be properly formatted. Many
blast-searchable
databases are available via your molbiol account.
To create your own blast-searchable databases to be used
with blastall, you need a file containing all of your sequences in fasta format. This data can then be
formatted for BLAST searching using a program provided with blastall called
formatdb.
Command line options
Table 1. General options available with blastall.
Table 2. Information on the different formatting options available with blastall.
Table 3. Information on the numbers that can be used with the -Q flag to invoke
alternative genetic codes when running blastx or tblastx searches.
Table 4. Further options for filtering
An example command line to run a blastp search of a peptide sequence called mypep.tfa,
against the swissprot database would be:
blastall -p blastp -d swissprot -i mypep.tfa -o mypep.blastp
Of course, you can add many other flags to get the type of search, and the type of output you want!
Table 1. General options available with blastall.
Flags shown in red are those that are necessary for blastall to
run.
| Flag
| Information required
| Type of information
| Default
| Other comments
|
| -p |
Program Name |
String (e.g. blastn, blastp, blastx, etc.) |
|
|
| -d |
DatabaseName |
String (e.g. embl, swissprot....etc.) |
nr |
default is not a viable choice on enterprise |
| -i |
Query filename |
Filename (and path if necessary) |
stdin |
|
| -o |
BLAST report Output filename |
Filename (and path if necessary) |
stdout (usually to screen) |
if you want your results saved into a file, you must specify a filename |
| -e |
Expectation value |
Real number |
10.0 |
|
| -m |
Alignment view options |
integer between 0 and 9 |
0 |
see Table 2 for more details |
| -F |
Filter query sequence |
T or F (for true or false) |
T (i.e. filtering is on) |
DUST is used with blastn, SEG with others |
| -G |
Cost to open a gap |
integer |
0 |
|
| -E |
Cost to extend a gap |
integer |
0 |
|
| -X |
X dropoff value for gapped alignment (in bits) |
integer |
0 |
|
| -I |
show GIs in deflines |
T or F (for true or false) |
F |
GI = NI in EMBL. Tracks versions of an entry. |
| -q |
Penalty for a nucleotide mismatch |
integer |
-3 |
for use with blastn only |
| -r |
Reward for a nucleotide match |
integer |
1 |
for use with blastn only |
| -v |
Number of one line descriptions |
integer |
500 |
|
| -f |
Threshold for extending hits |
integer |
0 |
|
| -b |
Number of alignments to show |
integer |
250 |
|
| -g |
Perfom gapped alignment |
T or F (for True or False) |
T |
not available with tblastx |
| -Q |
Query Genetic code to use |
integer |
1 (Universal) |
for blastx and tblast[nx] only |
| -D |
DB Genetic code |
integer |
1 (Universal) |
tblastn and tblastx only |
| -a |
number of processors to use |
integer |
1 |
|
| -O |
Seq. Align File |
Filename (and path if necessary) |
optional - no default |
|
| -J |
Believe the query defline |
T or F (for True or False) |
F |
|
| -M |
Matrix |
matrix name (and path if necessary) |
BLOSUM62 |
only certain combination of gap penalties and matrices are supported * |
| -W |
Word size |
integer |
0 |
default values are used if 0 is chosen. Defaults are 11 for
nucs and 3 for proteins ** |
| -z |
Effective length of the database |
integer |
0 |
0 means use the real size of the database (important for the statistics - leave as default) |
| -K |
Number of best hits from a region to keep |
integer |
100 |
|
| -P |
0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass |
integer |
0 |
|
| -Y |
Effective length of the search space |
real |
0.0 |
|
| -L |
Location on query sequence |
string |
|
|
| -S |
Query strands to search against database |
1(top strand),2(bottom strand) or 3(both) |
3 |
for blast[nx], and tblastx |
| -T |
Produce HTML output |
T or F (for True or False) |
F |
see Table 2 for more details |
| -l |
Restrict search of database to list of GIs |
string |
|
|
| -U |
use lower case filtering of FASTA sequence |
T or F (for True or False) |
F |
|
| -y |
Dropoff (X) for blast extensions in bits |
real |
0.0 |
|
| -Z |
X dropoff value for final gapped alignment (in bits) |
real |
0.0 |
|
| -R |
PSI-TBLASTN checkpoint file |
File In |
|
|
| -n |
Megablast search |
T or F (for True or False) |
F |
|
| -A |
Multiple Hits window size |
integer |
40 |
Zero for single hit algorithm |
* See NCBI notes for
more information on matrices and gap penalty combinations in BLAST.
** blastn will not work with a word size of less than 7
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Table 2. Information on the different formatting options available with
blastall.
Click on the flags to look at examples of the resulting output.
Note: These options are not available for tblastx
| Flag
| Formatting of BLAST alignments
|
| -m 0 |
pairwise |
| -m 1 |
master-slave showing identities |
| -m 2 |
master-slave no identities |
| -m 3 |
flat master-slave, show identities |
| -m 4 |
flat master-slave, no identities |
| -m 5 |
master-slave no identities and blunt ends |
| -m 6 |
flat master-slave, no identities and blunt ends |
| -m 7 |
XML Blast output |
| -m 8 |
tabular |
| -m 9 |
tabular with comment lines |
| -T T |
produce HTML Blast output |
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Table 3. Information on the numbers that can be used with the -Q flag to invoke
alternative genetic codes when running blastx or tblastx searches.
| Number
| Genetic code
|
| 1 |
standard or universal |
| 2 |
vertebrate mitochondrial |
| 3 |
yeast mitochondrial |
| 4 |
mold, protozoan, coelenterate mitochondrial and mycoplasma/spiroplasma |
| 5 |
invertebrate mitochondrial |
| 6 |
ciliate macronuclear |
| 9 |
echinodermate mitochondrial |
| 10 |
alternative ciliate macronuclear |
| 11 |
eubacterial |
| 12 |
alternative yeast |
| 13 |
ascidian mitochondrial |
| 14 |
flatworm mitochondrial |
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Table 4. Further options for filtering.
Further information about the actions of SEG and DUST can be found, here.
| Flag
| Filtering effects
| Example command
| Default values
|
| -F F |
Turn off all filtering |
|
|
| -F "S <window> <locut> <hicut>" |
Change the SEG options while running to values given after the letter S |
-F "S 10 1.0 1.5" |
Seg filters with a window=12, a locut=2.2, and a hicut= 2.5 |
| -F "C" |
Filter sequences using a coiled-coil filter |
|
|
| -F "C <window> <cutoff> <linker> |
Filter sequences using a coiled-coil filter and change the default settings for this filter |
-F "C 28 40.0 32" |
The default values are: window=22, cutoff=40/0, linker=32. The example command would change the window length only. |
| -F "C;S" |
Run both seg and coiled-coil filtering together |
|
|
| -F "D" |
Specify that you wish to filter using DUST |
|
|
| -F "m S" |
Specify that masking with SEG should only be done during the building of initial words. |
|
|
| -F "m D" |
Specify that masking with coiled-coil should only be done during the building of initial words. |
|
|
| -F "m C" |
Specify that masking with DUST should only be done during the building of initial words. |
|
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