nuget
LocalBLAST
01 Syntax
02 Methods
| Name | Overloads | Summary |
|---|---|---|
| .ctor | 1 | |
| Blastp | 1 | Generate the command line arguments of the program blastp. |
| GetLastLogFile | 1 | 返回BLAST程序的日志文件，本函数必须在执行完BLASTP或者BLASTN操作之后才可以调用，否则返回空对象 |
| FormatDb | 1 | |
| op_Implicit | 1 | |
| Blastn | 1 |
03 Properties
| Name | Overloads | Summary |
|---|---|---|
| EValue | 1 | Expectation value (E) [Real] Default = 10.0 |
| AlignmentView | 1 | Alignment view options, Range from 0 to 11: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4… |
| Filter | 1 | Filter query sequence (DUST with blastn, SEG with others) [String] Default = T |
| GapOpen | 1 | Cost to open a gap (-1 invokes default behavior) [Integer] Default = -1 |
| GapExtend | 1 | Cost to extend a gap (-1 invokes default behavior) [Integer] default = -1 |
| DropoffValue | 1 | X dropoff value for gapped alignment (in bits) (zero invokes default behavior) blastn 30, megablast 20, tblastx 0, all others 15 [Integer] default = 0 |
| GI | 1 | Show GI's in deflines [T/F] default = F |
| MismatchPenalty | 1 | Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3 |
| MatchReward | 1 | Reward for a nucleotide match (blastn only) [Integer] default = 1 |
| ForceLegacyNumber | 1 | Number of database sequences to show one-line descriptions for (V) [Integer] default = 500 |
| ConcatenatedQueriesNumber | 1 | Number of database sequence to show alignments for (B) [Integer] default = 250 |
| Threshold | 1 | Threshold for extending hits, default if zero blastp 11, blastn 0, blastx 12, tblastn 13 tblastx 13, megablast 0 [Real] default = 0 |
| GappedAlignment | 1 | Perform gapped alignment (not available with tblastx) [T/F] default = T |
| QueryGeneticCode | 1 | Query Genetic code to use [Integer] default = 1 |
| DBGeneticCode | 1 | DB Genetic code (for tblast[nx] only) [Integer] default = 1 |
| Processors | 1 | Number of processors to use [Integer] default = 1 |
| SeqAlign | 1 | SeqAlign file [File Out] Optional |
| QueryDeflineBelieve | 1 | Believe the query defline [T/F] default = F |
| Matrix | 1 | Matrix [String] default = BLOSUM62 |
| WordSize | 1 | Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer] default = 0 |
| DBEffectiveLength | 1 | Effective length of the database (use zero for the real size) [Real] default = 0 |
| BestHitsKeepsNumber | 1 | Number of best hits from a region to keep. |
| Hits | 1 | 0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer] default = 0 |
| SearchSpace | 1 | Effective length of the search space (use zero for the real size) [Real] default = 0 |
| Strand | 1 | Query strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] default = 3 |
| HTML | 1 | Produce HTML output [T/F] default = F |
| RestrictList | 1 | Restrict search of database to list of GI's [String] Optional |
| LowerCaseFiltering | 1 | Use lower case filtering of FASTA sequence [T/F] Optional |
| UngappedExtensionsXDropOff | 1 | X dropoff value for ungapped extensions in bits (0.0 invokes default behavior) blastn 20, megablast 10, all others 7 [Real] default = 0.0 |
| XDropoffValue | 1 | X dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 100, tblastx 0, all others 25 [Integer] default = 0 |
| CheckpointFile | 1 | PSI-TBLASTN checkpoint file [File In] Optional |
| MegaBlast | 1 | MegaBlast search [T/F] default = F |
| QueryLocation | 1 | Location on query sequence [String] Optional |
| HitsWindowSize | 1 | Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer] default = 0 |
| FrameShiftPenalty | 1 | Frame shift penalty (OOF algorithm for blastx) [Integer] default = 0 |
| IntronLength | 1 | Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. |
| ConcatenatedQueries | 1 | Number of concatenated queries, for blastn and tblastn [Integer] Optional default = 0 |
| ForceLegacy | 1 | Force use of the legacy BLAST engine [T/F] Optional default = F |
| CompositionBasedScoreAdjustments | 1 | Use composition-based score adjustments for blastp or tblastn: As first character: D or d: default (equivalent to T) 0 or F or f: no composition-based statistics 2 or T or t:… |
| SmithWatermanAlignments | 1 | Compute locally optimal Smith-Waterman alignments (This option is only available for gapped tblastn.) [T/F] default = F |
| MolTypeNucleotide | 1 | |
| MolTypeProtein | 1 |
04 Fields
| Name | Overloads | Summary |
|---|---|---|
| BLASTALLAssembly | 1 | The file path of the blastall program the in the BLAST+ program groups. |
| FormatDbAssembly | 1 | formatdb程序的文件名 |
| ARGUMS_BLASTP | 1 | The command line arguments of the blastp program. |
| ARGUMS_BLASTN | 1 | The command line arguments of the blastn program. |
05 Members
String)| Name | Type | Description |
|---|---|---|
BlastBin | String | Blast+ bin dir |
String, String, String, String)Generate the command line arguments of the program blastp. (生成blastp程序的命令行参数)
| Name | Type | Description |
|---|---|---|
Input | String | The target sequence FASTA file.(包含有目标待比对序列的FASTA文件) |
TargetDb | String | The selected database that to aligned.(将要进行比对的目标数据库) |
Output | String | - |
e | String | - |
返回BLAST程序的日志文件，本函数必须在执行完BLASTP或者BLASTN操作之后才可以调用，否则返回空对象
String, String)| Name | Type | Description |
|---|---|---|
Db | String | - |
dbType | String | "T" for protein, "F" for nucleotide. |
Expectation value (E) [Real] Default = 10.0
Alignment view options, Range from 0 to 11: 0 = pairwise, 1 = query-anchored showing identities, 2 = query-anchored no identities, 3 = flat query-anchored, show identities, 4 = flat query-anchored, no identities, 5 = query-anchored no identities and blunt ends, 6 = flat query-anchored, no identities and blunt ends, 7 = XML Blast output, 8 = tabular, 9 tabular with comment lines 10 ASN, text 11 ASN, binary [Integer] Default = 0
Filter query sequence (DUST with blastn, SEG with others) [String] Default = T
Cost to open a gap (-1 invokes default behavior) [Integer] Default = -1
Cost to extend a gap (-1 invokes default behavior) [Integer] default = -1
X dropoff value for gapped alignment (in bits) (zero invokes default behavior) blastn 30, megablast 20, tblastx 0, all others 15 [Integer] default = 0
Show GI's in deflines [T/F] default = F
Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3
Reward for a nucleotide match (blastn only) [Integer] default = 1
Number of database sequences to show one-line descriptions for (V) [Integer] default = 500
Number of database sequence to show alignments for (B) [Integer] default = 250
Threshold for extending hits, default if zero blastp 11, blastn 0, blastx 12, tblastn 13 tblastx 13, megablast 0 [Real] default = 0
Perform gapped alignment (not available with tblastx) [T/F] default = T
Query Genetic code to use [Integer] default = 1
DB Genetic code (for tblast[nx] only) [Integer] default = 1
Number of processors to use [Integer] default = 1
SeqAlign file [File Out] Optional
Believe the query defline [T/F] default = F
Matrix [String] default = BLOSUM62
Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer] default = 0
Effective length of the database (use zero for the real size) [Real] default = 0
Number of best hits from a region to keep. Off by default. If used a value of 100 is recommended. Very high values of -v or -b is also suggested [Integer] default = 0
0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer] default = 0
Effective length of the search space (use zero for the real size) [Real] default = 0
Query strands to search against database (for blast[nx], and tblastx) 3 is both, 1 is top, 2 is bottom [Integer] default = 3
Produce HTML output [T/F] default = F
Restrict search of database to list of GI's [String] Optional
Use lower case filtering of FASTA sequence [T/F] Optional
X dropoff value for ungapped extensions in bits (0.0 invokes default behavior) blastn 20, megablast 10, all others 7 [Real] default = 0.0
X dropoff value for final gapped alignment in bits (0.0 invokes default behavior) blastn/megablast 100, tblastx 0, all others 25 [Integer] default = 0
PSI-TBLASTN checkpoint file [File In] Optional
MegaBlast search [T/F] default = F
Location on query sequence [String] Optional
Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer] default = 0
Frame shift penalty (OOF algorithm for blastx) [Integer] default = 0
Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments. (0 invokes default behavior; a negative value disables linking.) [Integer] default = 0
Number of concatenated queries, for blastn and tblastn [Integer] Optional default = 0
Force use of the legacy BLAST engine [T/F] Optional default = F
Use composition-based score adjustments for blastp or tblastn:
As first character: D or d: default (equivalent to T) 0 or F or f: no composition-based statistics 2 or T or t: Composition-based score adjustments as in Bioinformatics 21:902-911, 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally For programs other than tblastn, must either be absent or be D, F or 0.
As second character, if first character is equivalent to 1, 2, or 3: U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only
default = D
Compute locally optimal Smith-Waterman alignments (This option is only available for gapped tblastn.) [T/F] default = F
The file path of the blastall program the in the BLAST+ program groups. (在BLAST+程序组之中的BLASTALL程序的文件路径)
formatdb程序的文件名
The command line arguments of the blastp program. (blastp程序的命令行参数)
The command line arguments of the blastn program.
String)String, String, String, String)