[Bioperl-l] Tiling of hsps using Bioperl

seidl-michael Seidl-Michael at t-online.de
Wed Oct 27 04:58:03 EDT 2010


Hi everyone,

I have a question about the Bio::Search::Tiling::MapTiling  package. I  
want to get the range of my tilled hsps using the "range" function.  
The reported range is, unfortunately, not what I would expect while  
looking at my data:

 >A
          Length = 1967

Score = 70.1 bits (170), Expect = 1e-11,   Method: Compositional  
matrix adjust.
Identities = 47/110 (42%), Positives = 66/110 (60%), Gaps = 29/110 (26%)

Query: 358   
EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVAR 417
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+++R+ AA A+        Q +++R
Sbjct: 1344 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVASMRS-AAIADV------- 
QTQLSR 1395

Query: 418  QEEDARRKEAARQEEVARELEVKSSMATKIQSHWRGTAARSEVSTLRAEA 467
                                 +++  A +IQS WRG  AR +V++LRAEA
Sbjct: 1396 ---------------------IENLTAVRIQSRWRGVLARVKVASLRAEA 1424



Score = 57.8 bits (138), Expect = 7e-08,   Method: Compositional  
matrix adjust.
Identities = 28/39 (71%), Positives = 33/39 (84%)

Query: 358  EAARQEEVARELEVKSSMATKIQSHWRGMAARSEVSTLR 396
            E ARQEE+AR+ E +S+MATKIQSHWRG  ARSEV+ LR
Sbjct: 1222 ELARQEELARQAEAESAMATKIQSHWRGSVARSEVAVLR 1260



Score = 47.4 bits (111), Expect = 1e-04,   Method: Compositional  
matrix adjust.
Identities = 43/115 (37%), Positives = 58/115 (50%), Gaps = 29/115 (25%)

Query: 299  
RELEVKSSMATKIQSHWRGMAARSEVSTLRAEAAAAEAAASEAARQEEVARQEEDARRKE 358
           +E + K+ MAT+IQS  RG+ AR        EA + + AASE        R + + RR++
Sbjct: 433 KETQRKNDMATQIQSGVRGVIAR--------EAYSEKLAASERI---- 
AIRIQTEFRRRQ 480

Query: 359 AARQEEVARE-----------------LEVKSSMATKIQSHWRGMAARSEVSTLR 396
           A +Q E  R+                  +   S ATKIQSHWRG  ARSEV+ LR
Sbjct: 481 AQKQLEALRQQLQREQTCAVVIQKILSSDSNESAATKIQSHWRGSVARSEVAVLR 535

I would expect to get [433,1424] when using:

my $tiling = Bio::Search::Tiling::MapTiling->new($hit);
my @range = $tiling->range('subject');

Instead my array includes [1344,535]. Do I have a conceptional problem  
with the function of "range" or is there something wired happening?

Thanks a lot for any help and suggestions,

Michael


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