[Bioperl-l] Blast Output and frac_aligned_query

[James Wasmuth]

First apologies if this has been debated before, didn;t see it in the 
archive and been away for a while, so unlcear on current state of affairs.

I have a bl2seq output (below) and when I extract its statistics, I am 
told that 156% of the query is aligned.

This is probably because of multiple HSP produced as the protein appears 
highly repetitive. Would this mess up the tiling the hsps, in its 
current implementation?


cheers
-james


e = 2e-19
s = 205
b = 83.6
aln_q = 1.56  !
aln_h = 0.09
id = 0.208
cons = 0.256
len = 332



> Query= prediction
>          (80 letters)
>
> >wormpep
>           Length = 2592
>
>  Score = 83.6 bits (205), Expect = 2e-19
>  Identities = 41/47 (87%), Positives = 43/47 (91%)
>
> Query: 1    SIRDEFSMNSAADSPMSTTGRPMVLTKAAMKAFNSTPPKKKNSSSGQ 47
>             SIRDEFSMNSAADSPMSTTGRPMVLTKAAMKAFNSTPPKK+   + Q
> Sbjct: 1528 SIRDEFSMNSAADSPMSTTGRPMVLTKAAMKAFNSTPPKKETDQAVQ 1574
>
>
>
>  Score = 29.3 bits (64), Expect = 0.004
>  Identities = 13/24 (54%), Positives = 18/24 (75%)
>
> Query: 50  SSSGSSSDSSSXDGSTSSDDSXDD 73
>            S S SSSDS S +GS+SS++  D+
> Sbjct: 493 SGSDSSSDSDSEEGSSSSNEDSDE 516
>
>
>
>  Score = 26.2 bits (56), Expect = 0.036
>  Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
>
> Query: 40  KKNSSSGQHDSSSGSSSDSSSXDGSTSSDDSXD 72
>            ++N++SG  DSSS S S+  S   +  SD+  D
> Sbjct: 488 QENNASGS-DSSSDSDSEEGSSSSNEDSDEQND 519
>
>
>
>  Score = 23.5 bits (49), Expect = 0.24
>  Identities = 14/69 (20%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
>
> Query: 9   NSAADSPMSTTGRPMV----LTKAAMKAFNSTPPKKKNSSSGQHDSSSGSSSDSSSXDGS 64
>            +  + SP S+  R  +     T+++++   +   ++ N+S     S S S   SSS + 
> Sbjct: 454 
> DQGSSSPSSSRDRQNLHDPLQTRSSVEHHTNQEDQENNASGSDSSSDSDSEEGSSSSNED 513
>
> Query: 65  TSSDDSXDD 73
>            +   +  D+
> Sbjct: 514 SDEQNDVDE 522
>
>
>
>  Score = 21.9 bits (45), Expect = 0.68
>  Identities = 10/29 (34%), Positives = 16/29 (55%)
>
> Query: 40  KKNSSSGQHDSSSGSSSDSSSXDGSTSSD 68
>            + +S + + ++  GSSS SSS D     D
> Sbjct: 443 RSSSPTSKSENDQGSSSPSSSRDRQNLHD 471
>
>
>
>  Score = 21.2 bits (43), Expect = 1.2
>  Identities = 13/34 (38%), Positives = 16/34 (47%)
>
> Query: 43   SSSGQHDSSSGSSSDSSSXDGSTSSDDSXDDXVP 76
>             S S    ++SGS S S +   STSS  S     P
> Sbjct: 2327 SRSSTMGNNSGSPSASGTTSPSTSSSISSGPDSP 2360
>
>
>
>  Score = 21.2 bits (43), Expect = 1.2
>  Identities = 12/47 (25%), Positives = 17/47 (36%)
>
> Query: 27   KAAMKAFNSTPPKKKNSSSGQHDSSSGSSSDSSSXDGSTSSDDSXDD 73
>             K   KA      KKK+      D S   S+D    D   S+ +   +
> Sbjct: 1144 KVRKKAEKEKLKKKKHRKGDSSDESDSDSNDELDLDVRKSTKEMTQE 1190
>
>
>
>  Score = 20.0 bits (40), Expect = 2.6
>  Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
>
> Query: 42  NSSSGQHDSSSGSSS-DSSSXDGSTSSDDSXDDXV 75
>            + SS   DS  GSSS +  S + +   ++  +D V
> Sbjct: 495 SDSSSDSDSEEGSSSSNEDSDEQNDVDEEDDEDVV 529
>
>
>
>  Score = 18.5 bits (36), Expect = 7.6
>  Identities = 7/14 (50%), Positives = 9/14 (64%)
>
> Query: 49   DSSSGSSSDSSSXD 62
>             +SS+G  SDS   D
> Sbjct: 1252 NSSNGEESDSEKAD 1265
>
>
> Lambda     K      H
>    0.294    0.109    0.279
>
> Gapped
> Lambda     K      H
>    0.267   0.0410    0.140
>
>
> Matrix: BLOSUM62
> Gap Penalties: Existence: 11, Extension: 1
> Number of Hits to DB: 2307
> Number of Sequences: 0
> Number of extensions: 39
> Number of successful extensions: 11
> Number of sequences better than 10.0: 1
> Number of HSP's better than 10.0 without gapping: 1
> Number of HSP's successfully gapped in prelim test: 0
> Number of HSP's that attempted gapping in prelim test: 0
> Number of HSP's gapped (non-prelim): 10
> length of query: 80
> length of database: 115,000
> effective HSP length: 56
> effective length of query: 24
> effective length of database: 114,944
> effective search space:  2758656
> effective search space used:  2758656
> T: 11
> A: 40
> X1: 17 ( 7.2 bits)
> X2: 38 (14.6 bits)
> X3: 64 (24.7 bits)
> S1: 35 (18.0 bits)
> S2: 35 (18.1 bits)


-- 
I like nonsense, it wakes up the brain cells.
		-- Dr. Seuss

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