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Old 11-17-2014, 01:40 AM   #1
Location: Hyderabad, India

Join Date: Apr 2010
Posts: 66
Default Basic Question about BLAST

Hi All,

I wanted to know the difference between HSPs and MSP in BLAST. Do multiple HSPs make up an MSP?

Secondly if two sequences (One query and another subject) have 2 HSPs/MSPs between them (HSPs are at two different locations), can I join the two HSPs/MSPs and say that the query covers [ (length(HSP1)+length(HSP2))/subject_length ] portion of the subject.

Finding it a little difficult to understand.

gen2prot is offline   Reply With Quote
Old 11-17-2014, 05:35 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

See the first para:

From: (Term MSP seems to have fallen out of favor in modern implementations of BLAST)

The fundamental unit of BLAST algorithm output is the High-
scoring Segment Pair (HSP). An HSP consists of two sequence
fragments of arbitrary but equal length whose alignment is
locally maximal and for which the alignment score meets or
exceeds a threshold or cutoff score. A set of HSPs is thus
defined by two sequences, a scoring system, and a cutoff
score; this set may be empty if the cutoff score is suffi-
ciently high.
A Maximal-scoring Segment Pair (MSP) is defined by two
sequences and a scoring system and is the highest-scoring of
all possible segment pairs that can be produced from the two
As for your second question: If non-overlapping parts of your query are covering two regions of the subject then you could say that query covers X% of the subject. You should not use coverage without providing a context of similarity/identity for the HSP.
GenoMax is offline   Reply With Quote

alignment global, blast, general

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