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The dialog is very similar to the dialog described in the Remote BLAST chapter, except the following parameters:
Select input file — this parameter is only presented if the dialog has been opened from the Tools main menu. Here you must input a query sequence file that would be used to search the BLAST database.
If the dialog has been opened e.g. using the Sequence View context menu, then the currently active sequence is used as a query sequence.
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following general options are available:
Select search - here you should select the tool you would like to use. If the query sequence is a nucleotide sequence then blastn, blastx and tblastx items are available. For a protein sequence the items are blastp and tblastn.Select database path —
Expectation value - this option specifies the statistical significance threshold for reporting matches against database sequences. Lower expect thresholds are more stringent, leading to fewer chance matches being reported.
Culling limit - the maximum number of hits that will be shown (not equal to number of annotations). The maximum availablle number is 5000.
Search for short, nearly exact matches - automatically adjusts the word size and other parameters to improve results for short queries.
Megablast - select this option to compare query with closely related sequences. It works best if the target percent identity is 95% or more, but it is very fast.
Database path - path to the database files.
Base name for BLAST DB files — - base name for the BLAST database files.
Number of CPUs being used — number of processors to use.
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You can see the description of the annotation saving parameters here.
The following advanced parameters are available:
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Word size - the size of the subsequence parameter for the initiated search.
Gap costs - costs to create and extend a gap in an alignment. Increasing the Gap costs will result in alignments which decrease the number of Gaps introduced.
Match scores - reward and penalty for matching and mismatching bases.
Filters - filters for regions of low compositional complexity and repeat elements of the human’s genome.
Masks for lookup table only — this option masks only for purposes of constructing the lookup table used by BLAST so that no hits are found based upon low-complexity sequence or repeats (if repeat filter is checked).
Mask lower case letters — with this option selected you can cut and paste a FASTA sequence in upper case characters and denote areas you would like filtered with lower case.
The following extension options are available:
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For gapped alignment - X dropoff value (in bits) for gapped alignment.
For ungapped alignment - X dropoff value (in bits) for ungapped alignment.
For final gapped alignment - X dropoff value (in bits) for final gapped alignment.
Multiple hits window size - multiple hits window size.
Perform gapped alignment - performs gapped alignment.