TBlastn Compares a protein query sequence against a nucleotide sequence database dynamically translated in all six reading frames (both strands) using the BLAST algorithm. The BLAST (Basic Local Alignment Search Tool) programs have been designed for speed to find high scoring local alignments. BLAST uses a heuristic algorithm which seeks local as opposed to global alignments and is therefore able to detect relationships among sequences which share only isolated regions of similarity (Altschul et al., 1990). Because of its design for speed, there may be a minimal loss of sensitivity to distant sequence relationships.

[TARGET SET] The target database(s) to search. Double-click the module or the value in the parameter table to access a list of available databases. CTRL-click to select multiple databases.

[EXPECTATION] The statistically significant expectation value. If the statistical significance ascribed to a match is greater than the E value, the match will not be reported. Lower E values are more stringent, leading to a fewer chance matches being reported.

[EXTEND PENALTY] The extend penalty for each character skipped in a gap including the first. Input 0 indicates default value.

[GAPPED ALIGNMENT] Specification on whether gapped alignment is to be performed or not.

• T if gapped alignment is to be performed
• F if gapped alignment is not to be performed.

[OPEN PENALTY] The open penalty for gap insertion. DeCypher uses this number as negative regardless of the sign specified. Input 0 indicates default value.  

[MATRIX] The scoring matrix file to use. These matrices are ASCII files and can have CRLF or LF line breaks. Use the matrix specified with filename. Nucleotide matrices have MNT extension and amino acid matrices have a .MAA extension. The full path must be specified.

[MAX ALIGNMENTS] The maximum number of target sequences that produced alignments to output.  Fewer alignments may be shown due to use of the [ALIGNMENT THRESHOLD] keyword.  There will never be more alignments than scores.  This number is the maximum for each query since each query has a separate list of alignments. This number corresponds to the number of target sequences; there may be multiple regions of similarity within a single target sequence and so the actual set of alignments may be larger than this number.

[NUM HITS] The maximum number of hits from a region to keep.  Previously this option was set to 100, meaning that if more than 100 HSP's had a hit to a region lower scoring ones would be dropped. The default is now zero, which turns off this behavior. In a few cases this change will result in more database sequences being reported. The previous behavior can be recovered by setting the value to 100. 

[EXTENSION DROPOFF] The dropoff (X) for the blast extensions in bits. 

[TARGET GIS] If specified, the search of the database will be restricted to this list of GIs. 

[REGION] The location on the query sequence to use. 

[QUERY FILTER] The specification on whether the query filter is to be used. The BLAST process filters your query sequence for low compositional complexity regions by default. Filtering can eliminate potentially confounding matches from the BLAST reports. OPTIONS:

• T if the query filter is to be used
• F if the query filter is not to be used

[THRESHOLD] The minimum score to output.  This allows a score or significance value to be specified as the threshold for displaying scores.  OPTIONS:

• n The minimum score to be displayed to n.
• Score = n The minimum score to be displayed to n.
• Significance = n The threshold is applied to reported E-value or P-score, or Z-score, whichever the user selected with the [SIGNIFICANCE] keyword.
• Score=n Significance=n Both a score threshold and a significance threshold must be met for the alignment to be displayed.

[WORD SIZE] The search word size.  The range of word sizes for amino acid jobs is 2 to 5.  Default: 3.

[X DROPOFF] X dropoff value for gapped alignment (in bits). 

[DB LENGTH] Effective length of the database. 0 indicates to use the real size. 

[SS LENGTH] Effective length of the search space. 0 indicates to use the real size.