MorusDB BLAST

Program: Database:  Expect:

More Parameters:

OUTPUT: STANDARD   [TABULAR   BEST HIT (>=1): BEST MATCH (>=1): ]

Enter sequence below in FASTA format (or enter MorusDB sequence IDs each with a prefix "ID:", for example, ID:Morus000035):

or load local sequence file in FASTA format:

      


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-G  Cost to open a gap (-1 invokes default behavior) [Integer], default = -1
-E  Cost to extend a gap (-1 invokes default behavior) [Integer], default = -1
-X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior):
    blastn 30, megablast 20, tblastx 0, all others 15 [Integer], default = 0
-I  Show GI's in deflines [T/F], default = F
-q  Penalty for a nucleotide mismatch (blastn only) [Integer], default = -3
-r  Reward for a nucleotide match (blastn only) [Integer], default = 1
-v  Number of database sequences to show one-line descriptions for (V) [Integer], default = 500
-b  Number of database sequence to show alignments for (B) [Integer], default = 250
-f  Threshold for extending hits, default if zero:
    blastp 11, blastn 0, blastx 12, tblastn 13, tblastx 13, megablast 0 [Real], default = 0
-g  Perform gapped alignment (not available with tblastx) [T/F], default = T
-Q  Query Genetic code to use [Integer], default = 1
-D  DB Genetic code (for tblast[nx] only) [Integer], default = 1
-J  Believe the query defline [T/F], default = F
-W  Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer], default = 0
-z  Effective length of the database (use zero for the real size) [Real], default = 0
-K  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
-P  0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer], default = 0
-Y  Effective length of the search space (use zero for the real size) [Real], default = 0
-S  Query strands to search against database (for blast[nx], and tblastx):
    3 is both, 1 is top, 2 is bottom [Integer], default = 3
-l  Restrict search of database to list of GI's [String]  Optional
-U  Use lower case filtering of FASTA sequence [T/F]  Optional
-y  X dropoff value for ungapped extensions in bits (0.0 invokes default behavior):
    blastn 20, megablast 10, all others 7 [Real], default = 0.0
-Z  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
-R  PSI-TBLASTN checkpoint file [File In]  Optional
-L  Location on query sequence [String]  Optional
-A  Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
    default = 0
-w  Frame shift penalty (OOF algorithm for blastx) [Integer], default = 0
-t  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
-B  Number of concatenated queries, for blastn and tblastn [Integer] Optional, default = 0
-V  Force use of the legacy BLAST engine [T/F] Optional, default = F
-C  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
      [String] default = D
-s  Compute locally optimal Smith-Waterman alignments
    (This option is only available for gapped tblastn.) [T/F], default = F

Program:     Expect:    More Parameters:

Sequence 1 in FASTA format (or enter a MorusDB sequence ID with a prefix "ID:", for example, ID:Morus000035):

or load local file 1

Sequence 2 in FASTA format (or enter a MorusDB sequence ID with a prefix "ID:", for example, ID:Morus000035):

or load local file 2

            


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-g  Gapped [T/F], default = T
-d  theor. db size (zero is real size) [Real], default = 0
-G  Cost to open a gap (-1 invokes default behavior) [Integer], default = -1
-E  Cost to extend a gap (-1 invokes default behavior) [Integer], default = -1
-X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior):
    blastn 30, megablast 20, tblastx 0, all others 15 [Integer], default = 0
-W  Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer], default = 0
-q  Penalty for a nucleotide mismatch (blastn only) [Integer], default = -3
-r  Reward for a nucleotide match (blastn only) [Integer], default = 1
-F  Filter query sequence (DUST with blastn, SEG with others) [String], default = T
-e  Expectation value (E) [Real], default = 10.0
-S  Query strands to search against database (blastn only). 3 is both, 1 is top, 2 is bottom [Integer]
    default = 3
-m  Use Mega Blast for search [T/F]  Optional, default = F
-Y  Effective length of the search space (use zero for the real size) [Real], default = 0
-t  Length of the largest intron allowed in tblastn for linking HSPs [Integer], default = 0
-I  Location on first sequence [String]  Optional
-J  Location on second sequence [String]  Optional
-D  Output format: 0 - traditional, 1 - tabular [Integer], default = 0
-U  Use lower case filtering for the query sequence [T/F]  Optional, default = F
-V  Force use of the legacy BLAST engine [T/F]  Optional, default = F

Program: Database:  Expect:

More Parameters:

OUTPUT: STANDARD   [TABULAR   BEST HIT (>=1): BEST MATCH (>=1): ]

Enter sequence below in FASTA format (or enter MorusDB sequence IDs each with a prefix "ID:", for example, ID:Morus000035):

or load local sequence file in FASTA format:

      


CLICK HERE TO SHOW MORE PARAMETERS
-G  Cost to open a gap (zero invokes default behavior) [Integer]
    default = 0
-E  Cost to extend a gap (zero invokes default behavior) [Integer]
    default = 0
-X  X dropoff value for gapped alignment (in bits) (zero invokes default behavior) [Integer]
    default = 0
-I  Show GI's in deflines [T/F]
    default = F
-q  Penalty for a nucleotide mismatch (blastn only) [Integer]
    default = -3
-r  Reward for a nucleotide match (blastn only) [Integer]
    default = 1
-v  Number of one-line descriptions (V) [Integer]
    default = 500
-b  Number of alignments to show (B) [Integer]
    default = 250
-f  Threshold for extending hits, default if zero [Integer]
    default = 0
-g  Perform gapped alignment (not available with tblastx) [T/F]
    default = T
-Q  Query Genetic code to use [Integer]
    default = 1
-D  DB Genetic code (for tblast[nx] only) [Integer]
    default = 1
-W  Word size, default if zero [Integer]
    default = 0
-z  Effective length of the database (use zero for the real size) [Real]
    default = 0
-P  0 for multiple hits 1-pass, 1 for single hit 1-pass [Integer]
    default = 0
-Y  Effective length of the search space (use zero for the real size) [Real]
    default = 0
-S  Query strands to search against database (for blast[nx], and tblastx).
    3 is both, 1 is top, 2 is bottom [Integer]
    default = 3
-U  Use lower case filtering of FASTA sequence [T/F]  Optional
    default = F
-A  Multiple Hits window size, default if zero (blastn 0, all others 40 [Integer])
    default = 0
-t  Length of the largest intron allowed in tblastn for linking HSPs (0 disables linking) [Integer]
    default = 0