A BLAST run comprises, among other sections, a ‘ranking’ of hits with one-line summaries including scoring information, followed by the search database ‘hits’ themselves. Each hit may contain one or more HSPs (ungapped BLAST) or gapped alignments (gapped BLAST), not all of which may be reported in the ranking.
Some control over which HSPs are to be processed by MView is provided by the command line option -hsp. There are three choices:
MView option Description -hsp ranked Only those HSPs or alignments that contributed to the ranked hit are selected. These are tiled into a single alignment row per hit. This is the default behaviour. -hsp discrete All HSPs or alignments are selected, but each is assigned its own row in the resulting stacked alignment. This is way to view or extract every distinct HSP. -hsp all All HSPs or alignments are selected and tiled into a single alignment row per hit. This is probably not what you want and the option may be removed in future.
Precise application of these processing modes varies slightly with each BLAST program because properties such as query and/or hit nucleotide strand orientation or reading frame must be taken into consideration.
The ranking contains scoring information for the best alignment fragment comprising a score (score or bits, depending on BLAST version), an estimate of significance (E-value or p-value, depending on version) and an optional fragment count, N.
Each database search hit comprises 1 or more fragments or HSPs, each of which has a corresponding score, significance level and the fragment count, N. These are grouped by significance and fragment count and are generally ordered by decreasing score (best first).
Very often there may be just one alignment per hit and this is extracted and output by MView. Otherwise, in ranked mode (the default), MView applies the following algorithm to choose HSPs to tile.
Select the ranked HSPs
Select a sequentially coherent subset
Strip query gaps
Tile
Clashes lead to small discrepancies in the affected sequences and occur when overlapping fragments have:
The -hsp discrete mode can be used to output each HSP in its own alignment row, and will report all HSPs, including the alternative ones with other significance scores.
Lastly, if you need a real sequence alignment, use the information provided by MView to choose sequence identifiers then use a proper multiple alignment tool such as CLUSTAL on the original sequences.
A more detailed description of the selection rules is given for each BLAST family and program, as follows: