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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 view of the Advanced options tab depends on the selected search. For the blastn search it looks like on the picture above. When the blastx search is selected in the general options, the view of the Advanced options tab is the following:
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<center>
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<img src="/wiki/download/attachments/14059181/Making Request to Database_2_0.png"/>
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As you can see there is no Match scores option, but there are Threshold, Matrix, Composition-based statistics and Service options.
Threshold - threshold for extending hits.
Matrix — key element in evaluating the quality of a pair-wise sequence alignment is the “substitution matrix”, which assigns a score for aligning any possible pair of residues.
Service — blastp service which needs to be performed: plain, psi or phi.
Composition-based statistics - composition-based statistics.
When the tblastx search is selected in the general options, the view of the Advanced options tab is the following:
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<center>
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<img src="/wiki/download/attachments/14059181/Making Request to Database_2_1.png"/>
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The following extension options are available:
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