parsing blastp output using biopython

Question

I need help to parse the following blastp output for aligning 2 sequences:

BLASTP 2.2.28+


Query= 
Length=237

Subject= 
Length=268


 Score =  429 bits (1104),  Expect = 2e-157, Method: Compositional matrix adjust.
 Identities = 237/268 (88%), Positives = 237/268 (88%), Gaps = 31/268 (12%)

Query  1    MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVP-------  53
            MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVP       
Sbjct  1    MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLAD  60

Query  54   --TIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQ  111
              TIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQ
Sbjct  61   GPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQ  120

Query  112  VGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYL----  167
            VGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYL    
Sbjct  121  VGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRS  180

Query  168  ---------------LIEKLKEYHAAPALQG-GISSPEQVSAAVRAGAAGAISGSAIVKI  211
                           LIEKLKEYHAAPALQG GISSPEQVSAAVRAGAAGAISGSAIVKI
Sbjct  181  GVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKI  240

Query  212  IEKNLASP--MLAELRSFVSAMKAASRA  237
            IEKNLASP  MLAELRSFVSAMKAASRA
Sbjct  241  IEKNLASPKQMLAELRSFVSAMKAASRA  268



Lambda      K        H        a         alpha
   0.320    0.136    0.386    0.792     4.96 

Gapped
Lambda      K        H        a         alpha    sigma
   0.267   0.0410    0.140     1.90     42.6     43.6 

Effective search space used: 51972




Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Neighboring words threshold: 11
Window for multiple hits: 40

What did you try? What problems do you have? Did you check the biopython tutorial? — llrs, Oct 06 '14 at 10:08

score 0 · Answer 1 · answered Oct 06 '14 at 12:16

You have to read this entry in the Tutorial: http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec100

You will learn how to launch a BLAST locally and get a XML output. Once you have your XML file (and not the text you pasted in your question), you can parse it with:

NCBIXML.parse(xml_results)

parsing blastp output using biopython

1 Answers1