Basic Question about BLAST

[gen2prot]

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.

thanks
Abhijit

[GenoMax]

See the first para: http://www.cs.cmu.edu/~durand/03-711...st2013Oct8.pdf

From: http://dir.nhlbi.nih.gov/papers/lkem...last_help.html (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
sequences.

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.