[Bioperl-l] Parsing strand and frame for blastx results using SearchIO

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Jul 23 11:49:21 EDT 2008


Hello

Am currently using bioperl-1.5.2_102 and BLASTX 2.2.17 [Aug-26-2007],
but this also holds true in 1.5.1 and 1.4.0.

I have a results file that is pasted below, and a script that is also
pasted below - just wondering how searchIO thinks the strand is 0 and
the frame is 2?

Result:
BLASTX 2.2.17 [Aug-26-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.
Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= lcl|chr2 42223489  - 44537930
         (2,314,442 letters)

Database: ../chemokine_receptors_aa.txt 
           15 sequences; 5543 total letters

Searching..................................................done



                                                                 Score
E
Sequences producing significant alignments:                      (bits)
Value

chCCRc
727   0.0  

>chCCRc 
          Length = 377

 Score =  727 bits (1877), Expect = 0.0
 Identities = 362/377 (96%), Positives = 362/377 (96%)
 Frame = -3

Query: 496563
MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 496384
 
MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK
Sbjct: 1
MEQRKKLTGRHTRALYLWFFPSQESKMNPTDLFLSTTEYDYGYDENTAPCNEGNSFPRFK 60

Query: 496383
SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 496204
 
SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY
Sbjct: 61
SLFLPILYCLVFVFCLLGNSLVLWILLTRKRLMTMTDICLLNLAASDLLFIVPLPFQAYY 120

Query: 496203
ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 496024
 
ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS
Sbjct: 121
ASDQWVFGNALCKIMGGIYYTGFYSSIFFITLMSIDRYIAIVHAVYAMKIRTASCGTMIS 180

Query: 496023
LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 495844
 
LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL
Sbjct: 181
LVLWLVAGLASVPNIVFNQQLEIEQSVQCVPVYPPGNNIWKVTTQFAANILGLLIPFSIL 240

Query: 495843
IHCYAQILRNLRKCKNQNXXXXXXXXXXXXXXXFLFWTPFNVVLFLDSLQSLLIIDNCQA 495664
              IHCYAQILRNLRKCKNQN
FLFWTPFNVVLFLDSLQSLLIIDNCQA
Sbjct: 241
IHCYAQILRNLRKCKNQNKIKAIKMIFIIVIVFFLFWTPFNVVLFLDSLQSLLIIDNCQA 300

Query: 495663
SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 495484
 
SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS
Sbjct: 301
SSQITLALQLTETISFIHCCLNPVIYAFAGVTFKAHLKRLLQPCARILWSPTRGSGVTQS 360

Query: 495483 SLVLSQISGCSDSAGVL 495433
              SLVLSQISGCSDSAGVL
Sbjct: 361    SLVLSQISGCSDSAGVL 377


  Database: ../chemokine_receptors_aa.txt
    Posted date:  Jul 23, 2008  2:43 PM
  Number of letters in database: 5543
  Number of sequences in database:  15
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 15
Number of Hits to DB: 28,029,184
Number of extensions: 721812
Number of successful extensions: 2651
Number of sequences better than 1.0e-05: 15
Number of HSP's gapped: 2358
Number of HSP's successfully gapped: 148
Length of query: 771480
Length of database: 5543
Length adjustment: 102
Effective length of query: 771378
Effective length of database: 4013
Effective search space: 3095539914
Effective search space used: 3095539914
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 33 (17.3 bits)


Script:
#!/usr/bin/perl

use lib "/usr/local/bioperl-1.5.2_102";
use Bio::SearchIO;

my $searchio = Bio::SearchIO->new(-format => 'blast', -file =>
"test.blast");

while (my($result) = $searchio->next_result()) {
	unless (defined $result) {
		# there is an undefined result at the end of SearchIO
objects
		last;
	}

	while(my $hit = $result->next_hit) {
		while (my $hsp = $hit->next_hsp) {
		
			print $hit->name, "\t";
			print $hsp->strand('hit'), "\t";
			print $hsp->frame, "\n";
		}
	}
}

Output:
-bash-3.00$ perl parse_test_blast.pl
chCCRc  0       2


Head of Informatics
Institute for Animal Health
Compton
Berks
RG20 7NN
01635 578411 

http://www.iah.ac.uk/research/bioinformatics/bioinf.shtml

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